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Zhao T, Cai X, Zhang S, Wang M, Chen L, Li X, Wang Z, Wang L, Jiang W, Ha Y, Li H, Liu Y, Lu Q, Cui F. COVID-19 vaccine hesitancy in Chinese residents: A national cross-sectional survey in the community setting. Hum Vaccin Immunother 2025; 21:2481003. [PMID: 40156199 PMCID: PMC11959896 DOI: 10.1080/21645515.2025.2481003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Revised: 03/01/2025] [Accepted: 03/14/2025] [Indexed: 04/01/2025] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine hesitancy is associated with community aggregation, inducing low vaccine coverage and potentially more frequent community-level outbreak. Addressing vaccine hesitancy in community settings should be a priority for healthcare providers. A cross-sectional online questionnaire survey was conducted during June and July 2022. Ten sites were set up in eastern, central, and western China, from where residents were recruited in a community setting. In total, 7,241 residents from 71 communities were included. Of the residents, 7.0% had refusal administration, 30.4% had delayed administration, and community clustering accounted for 2.4-3.7% and 8.5-9.6% of the variation, respectively. The reasons for primary-dose refusal were diseases, pregnancy, or lactation, whereas the main reasons for booster-dose refusal were diseases during the vaccination period, no time to vaccinate, and felt unnecessary to vaccinate. Younger age (under 40), female, residing in urban settings and having self-reported diseases were sociodemographic indicators of risk for refusal. In the health belief model of refusing to vaccinate, perceived barriers had a positive impact on refusal (β = 0.08), while perceived benefits had a negative impact (β = -0.09). In conclusion, this study underscores the population heterogeneity and community clustering of SARS-CoV-2 vaccine hesitancy. Targeted interventions for these high-risk groups are crucial to enhance vaccination coverage and prevent outbreaks. Public health strategies should address vaccine hesitancy at different stages and doses, while considering both individual beliefs and community dynamics.
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Affiliation(s)
- Tianshuo Zhao
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Xianming Cai
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Sihui Zhang
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Mingting Wang
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Linyi Chen
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Xikun Li
- The First Psychiatric Hospital of Harbin, Harbin, Heilongjiang, P. R. China
| | - Zhuangye Wang
- Dezhou Center for Disease Control and Prevention, Dezhou, Shandong, P. R. China
| | - Li Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, Anhui, P. R. China
| | - Wenguo Jiang
- Jining Center for Disease Control and Prevention, Jining, Shandong, P. R. China
| | - Yu Ha
- Jiuzhaigou Center for Disease Control and Prevention, Aba, Sichuan, P. R. China
| | - Hui Li
- Gansu Provincial Center for Disease Control and Prevention, Laznhou, Gansu, P. R. China
| | - Yaqiong Liu
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Qingbin Lu
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
| | - Fuqiang Cui
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, P. R. China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, P. R. China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, P. R. China
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2
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Tang H, Zhuo Y, Chen J, Zhang R, Zheng M, Huang X, Chen Y, Huang M, Zeng Z, Huang X, Han C, Huang Y. Immune evasion, infectivity, and membrane fusion of the SARS-CoV-2 JN.1 variant. Virol J 2025; 22:162. [PMID: 40413500 PMCID: PMC12103042 DOI: 10.1186/s12985-025-02737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Accepted: 04/10/2025] [Indexed: 05/27/2025] Open
Abstract
SARS-CoV-2 undergoes continuous mutations during transmission, resulting in a variety of Omicron subvariants. Currently, SARS-CoV-2 BA.2.86 and its descendants JN.1, KP.2, KP.1.1 have been identified as the primary variants spreading globally. These emerging Omicron variants have increased transmissibility, potentially elevating the risk of viral reinfection in the population. However, the biological characteristics of newly-emerged Omicron subvariants in infecting host cells remain unclear. In this study, we assessed the neutralization effect of BA.2.86 and its descendant JN.1, as well as D614G, BA.2, BA.4/5, XBB.1.5, EG.5.1, HV.1, HK.3, JD.1.1 and JG.3 on convalescent sera obtained from individuals infected with BA.5 or XBB.1.5 strain. We evaluated the biological characteristics of variants spike proteins by measuring viral infectivity, affinity for receptors, and membrane fusion. Compared to XBB-related subvariants, BA.2.86 exhibited a diminished immune escape response, but JN.1 displayed a markedly augmented immune escape capability, which was closely related to its rapid transmission. BA.2.86 was less infectious in susceptible cells, while the JN.1 variant exhibited relatively high infectivity. Notably, BA.2.86 and JN.1 exhibited low fusion activity in 293 T-ACE2 cells, but relatively high fusogenicity in transmembrane protease serine 2 (TMPRSS2) overexpression cells. This study explored the evolutionary characteristics of emerging Omicron subvariants in host adaptation, and provided new strategies for the prevention and treatment of coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Haijun Tang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Yanhang Zhuo
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Rongzhao Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Miao Zheng
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350001, China
| | - Xinghua Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Yisheng Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Minjian Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Zhaonan Zeng
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Xueping Huang
- Department of Gastroenterology, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, China.
- Department of Gastroenterology, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
| | - Chenfeng Han
- Department of Blood Transfusion, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China.
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Fujian Provincial Key Laboratory of Cardiovascular Disease, Fujian Provincial Key Laboratory of Critical Care Medicine, Fuzhou, Fujian, 350001, China.
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3
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Zhao T, Lei Y, Liu C, Zhang D, Li K, Shan S, Li C, Wei Z, Yang Y, Zhang T, Sun K, Sun H, Zhang L, Liu P. A Versatile High-Throughput Single-Cell Screening Platform for Profiling Antigen-Specific Long-Lived B Cells in Blood and Bone Marrow. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2414945. [PMID: 40202243 DOI: 10.1002/advs.202414945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 03/20/2025] [Indexed: 04/10/2025]
Abstract
Antigen-specific B cells play a crucial role in the long-term immune response following infection or vaccination, differentiating into antibody-secreting cells (ASCs) and memory B cells (MBCs). However, profiling ASCs is challenging primarily due to their lack of membrane-bound surface B cell receptors. In this study, the Modular Superhydrophobic Microwell Array Chip (MoSMAR-chip) is introduced as a versatile, cost-effective, and high-throughput platform for identifying and characterizing individual antigen-specific ASCs and MBCs at the single-cell level within seven days. Using this platform, comprehensive analyses of single ASCs could be performed from bone marrows of coronavirus disease 2019 (COVID-19) vaccine-immunized mice and a diverse set of antibodies capable of neutralizing the highly divergent JN1 variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. These results demonstrate that the MoSMAR-chip facilitates efficient single-cell multi-omics and functional analyses of antigen-specific ASCs, offering a powerful tool for investigating complex long-term B cell immunity in diverse clinical conditions, such as infectious diseases, autoimmunity, and beyond.
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Affiliation(s)
- Tian Zhao
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuqing Lei
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
| | - Chang Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Dong Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Kaiyi Li
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Sisi Shan
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
| | - Chenyu Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
| | - Zimeng Wei
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
| | - Yuhan Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
| | - Ting Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Kai Sun
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Haoran Sun
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Peng Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- Changping Laboratory, Beijing, 102206, China
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4
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Purushotham JN, Lutz HL, Parker E, Andersen KG. Immunological drivers of zoonotic virus emergence, evolution, and endemicity. Immunity 2025; 58:784-796. [PMID: 40168990 PMCID: PMC11981831 DOI: 10.1016/j.immuni.2025.03.014] [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: 10/10/2024] [Revised: 03/11/2025] [Accepted: 03/12/2025] [Indexed: 04/03/2025]
Abstract
The disruption of natural ecosystems caused by climate change and human activity is amplifying the risk of zoonotic spillover, presenting a growing global health threat. In the past two decades, the emergence of multiple zoonotic viruses has exposed critical gaps in our ability to predict epidemic trajectories and implement effective interventions. RNA viruses, in particular, are challenging to control due to their high mutation rates and ability to adapt and evade immune defenses. To better prepare for future outbreaks, it is vital that we deepen our understanding of the factors driving viral emergence, transmission, and persistence in human populations. Specifically, deciphering the interactions between antibody-mediated immunity and viral evolution will be key. In this perspective, we explore these dynamic relationships and highlight research priorities that may guide the development of more effective strategies to mitigate the impact of emerging infectious diseases.
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Affiliation(s)
- Jyothi N Purushotham
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Research Translational Institute, La Jolla, CA, USA
| | - Holly L Lutz
- Denver Museum of Nature and Science, Denver, CO, USA
| | - Edyth Parker
- The Institute of Genomics and Global Health (IGH), Redeemer's University, Ede, Osun, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Research Translational Institute, La Jolla, CA, USA.
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5
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Fu W, Zhang W, You Z, Li G, Wang C, Lei C, Zhao J, Hou J, Hu S. T-Cell-Dependent Bispecific IgGs Protect Aged Mice From Lethal SARS-CoV-2 Infection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2406980. [PMID: 39976129 PMCID: PMC12005765 DOI: 10.1002/advs.202406980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 01/04/2025] [Indexed: 02/21/2025]
Abstract
T-cell ageing may be a key factor in the disproportionate severity of coronavirus disease 2019 (COVID-19) in older populations. For hospitalized COVID-19 patients, treatment involving the use of monoclonal antibodies with the ability to neutralize SARS-CoV-2 usually involves the administration of high doses but has not been very effective at preventing complications or fatality, highlighting the need for additional research into anti-SARS-CoV-2 therapies, particularly for older populations. In this study, it is discovered that older persons with a severe SARS-CoV-2 infection has weaker T-cell responses. Therefore the development and characterization of spike-targeting T-cell-dependent bispecific (TDB) full-length human immunoglobulin Gs with enhanced efficacy in the treatment of COVID-19 is described. Using S-targeting TDBs, polyclonal T cells are guided to target and destroy S-expressing cells, preventing the cell-to-cell transmission of SARS-CoV-2 and thereby eliminating the need for SARS-CoV-2-specific immunity. Using animal models of COVID-19, it is shown that the selective activation of T cells improves the efficiency of treatment in preinfected mice by attenuating disease-induced weight loss and death. The significance of T-cell-based immunity during infection is highlighted by the findings. These results have implications for better clinical effectiveness of therapies for COVID-19 and the development of T-cell-dependent medicines for the elderly population.
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Affiliation(s)
- Wenyan Fu
- Department of Assisted ReproductionShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghai200011China
- Department of Biomedical EngineeringCollege of Basic Medical SciencesSecond Military Medical UniversityShanghai200433China
| | - Wei Zhang
- Department of Respiratory and Critical Care MedicineFirst Affiliated HospitalSecond Military Medical UniversityShanghai200433China
- Center of Critical Care MedicineFirst Affiliated Hospitalthe Second Military Medical UniversityShanghai200433China
| | - Zhongshuai You
- Department of Biomedical EngineeringCollege of Basic Medical SciencesSecond Military Medical UniversityShanghai200433China
| | - Guangyao Li
- Department of BiophysicsCollege of Basic Medical, SciencesSecond Military Medical UniversityShanghai200433China
| | - Chuqi Wang
- Department of Biomedical EngineeringCollege of Basic Medical SciencesSecond Military Medical UniversityShanghai200433China
| | - Changhai Lei
- Department of BiophysicsCollege of Basic Medical, SciencesSecond Military Medical UniversityShanghai200433China
| | - Jian Zhao
- KOCHKOR Biotech, Inc.Shanghai201406China
| | - Jin Hou
- National Key Laboratory of Medical Immunology and Institute of ImmunologySecond Military Medical UniversityShanghai200433China
| | - Shi Hu
- Department of Biomedical EngineeringCollege of Basic Medical SciencesSecond Military Medical UniversityShanghai200433China
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6
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Yuan M, Wilson IA. Structural Immunology of SARS-CoV-2. Immunol Rev 2025; 329:e13431. [PMID: 39731211 PMCID: PMC11727448 DOI: 10.1111/imr.13431] [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: 11/07/2024] [Accepted: 12/10/2024] [Indexed: 12/29/2024]
Abstract
The SARS-CoV-2 spike (S) protein has undergone significant evolution, enhancing both receptor binding and immune evasion. In this review, we summarize ongoing efforts to develop antibodies targeting various epitopes of the S protein, focusing on their neutralization potency, breadth, and escape mechanisms. Antibodies targeting the receptor-binding site (RBS) typically exhibit high neutralizing potency but are frequently evaded by mutations in SARS-CoV-2 variants. In contrast, antibodies targeting conserved regions, such as the S2 stem helix and fusion peptide, exhibit broader reactivity but generally lower neutralization potency. However, several broadly neutralizing antibodies have demonstrated exceptional efficacy against emerging variants, including the latest omicron subvariants, underscoring the potential of targeting vulnerable sites such as RBS-A and RBS-D/CR3022. We also highlight public classes of antibodies targeting different sites on the S protein. The vulnerable sites targeted by public antibodies present opportunities for germline-targeting vaccine strategies. Overall, developing escape-resistant, potent antibodies and broadly effective vaccines remains crucial for combating future variants. This review emphasizes the importance of identifying key epitopes and utilizing antibody affinity maturation to inform future therapeutic and vaccine design.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
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7
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Nan X, Li Y, Zhang R, Wang R, Lv N, Li J, Chen Y, Zhou B, Wang Y, Wang Z, Zhu J, Chen J, Li J, Chen W, Zhang Q, Shi X, Zhao C, Chen C, Liu Z, Zhao Y, Liu D, Wang X, Yan LT, Li T, Zhang L, Yang YR. Exploring distinct modes of inter-spike cross-linking for enhanced neutralization by SARS-CoV-2 antibodies. Nat Commun 2024; 15:10578. [PMID: 39632831 PMCID: PMC11618796 DOI: 10.1038/s41467-024-54746-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 11/19/2024] [Indexed: 12/07/2024] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when binds fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, enriching our understanding of enhanced neutralization by SARS-CoV-2 antibodies.
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Grants
- 22277017, 92169205, 82241072, 82150205, and 32270983 National Natural Science Foundation of China (National Science Foundation of China)
- National Key R&D Program of China (2022YFA1206400), Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDB0770000), National Key Plan for Scientific Research and Development of China (2022YFF1203100, 2021YFC0864500,2022YFC2604100,2022YFC2303400 and 2023YFC3043300), the Wanke Scientific Research Program (20221080056), Special Research Fund for the Central High-level Hospitals of Peking Union Medical College Hospital (2022-PUMCH-D-008), the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (2021-I2M-1-037), National Key Technologies R&D Program for the 13th Five-year Plan (2017ZX10202101-001), CAMS Innovation Fund for Medical Sciences (CIFMS 2019-I2M-5-018),Tencent Foundation, Shuidi Foundation, and TH Capital for financial support.
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Affiliation(s)
- Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Yujie Li
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
| | - Rui Zhang
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ruoke Wang
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Niannian Lv
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiayi Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfang Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bini Zhou
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
| | - Jing Chen
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinqian Li
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Wenlong Chen
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Qi Zhang
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Changwen Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Chunying Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
| | - Zhihua Liu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuliang Zhao
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing, China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China.
- Center for AIDS Research, Chinese Academy of Medical Sciences, Beijing, China.
| | - Linqi Zhang
- Comprehensive AlDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University, Beijing, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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8
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Liu H, Chen P, Zhai X, Huo KG, Zhou S, Han L, Fan G. PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery. Sci Data 2024; 11:1316. [PMID: 39627219 PMCID: PMC11615212 DOI: 10.1038/s41597-024-03997-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 10/11/2024] [Indexed: 12/06/2024] Open
Abstract
Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.
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Affiliation(s)
- Huaqing Liu
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, 510700, China
| | - Peiyi Chen
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, 510700, China
| | - Xiaochen Zhai
- Cyagen Biosciences (Suzhou) Inc., Guangzhou, 215000, China
| | - Ku-Geng Huo
- Cyagen Biosciences (Guangzhou) Inc., Guangzhou, 510700, China
| | - Shuxian Zhou
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, 510700, China
| | - Lanqing Han
- Artificial Intelligence Innovation Center, Research Institute of Tsinghua, Pearl River Delta, Guangzhou, 510700, China.
- Cyagen Biomodels (Guangzhou) Co., Ltd, Guangzhou, 510700, China.
| | - Guoxin Fan
- Department of Pain Medicine, Shenzhen Nanshan People's Hospital, Shenzhen University Medical School, Shenzhen, 518056, China.
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9
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Niu X, Li Z, Wang J, Jian F, Yu Y, Song W, Yisimayi A, Du S, Zhang Z, Wang Q, Wang J, An R, Wang Y, Wang P, Sun H, Yu L, Yang S, Xiao T, Gu Q, Shao F, Wang Y, Xiao J, Cao Y. Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain. Emerg Microbes Infect 2024; 13:2412990. [PMID: 39361729 PMCID: PMC11520098 DOI: 10.1080/22221751.2024.2412990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/02/2024] [Indexed: 10/05/2024]
Abstract
A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wild-type or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results revealed the function of the indels in the NTD of BA.2.86/JN.1 sublineage in evading neutralizing antibodies and highlighted the importance of considering the immunogenicity of NTD in vaccine design.
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Affiliation(s)
- Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China
| | - Zhiqiang Li
- Changping Laboratory, Beijing, People’s Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China
| | - Yuanling Yu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Shuo Du
- Changping Laboratory, Beijing, People’s Republic of China
| | - Zhiying Zhang
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, People’s Republic of China
| | - Qianran Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Jing Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Ran An
- Changping Laboratory, Beijing, People’s Republic of China
| | - Yao Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Peng Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Haiyan Sun
- Changping Laboratory, Beijing, People’s Republic of China
| | - Lingling Yu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Qingqing Gu
- Changping Laboratory, Beijing, People’s Republic of China
| | - Fei Shao
- Changping Laboratory, Beijing, People’s Republic of China
| | - Youchun Wang
- Changping Laboratory, Beijing, People’s Republic of China
| | - Junyu Xiao
- Changping Laboratory, Beijing, People’s Republic of China
- School of Life Sciences, Peking University, Beijing, People’s Republic of China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing, People’s Republic of China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, People’s Republic of China
- Changping Laboratory, Beijing, People’s Republic of China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing, People’s Republic of China
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10
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Baker CN, Duso D, Kothapalli N, Hart T, Casey S, Cookenham T, Kummer L, Hvizdos J, Lanzer K, Vats P, Shanbhag P, Bell I, Tighe M, Travis K, Szaba F, Harder JM, Bedard O, Oberding N, Ward JM, Adams MD, Lutz C, Bradrick SS, Reiley WW, Rosenthal NA. Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19. Sci Rep 2024; 14:25147. [PMID: 39448712 PMCID: PMC11502910 DOI: 10.1038/s41598-024-77087-1] [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: 07/02/2024] [Accepted: 10/18/2024] [Indexed: 10/26/2024] Open
Abstract
Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a few other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad spectrum of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.
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Affiliation(s)
| | - Debra Duso
- Trudeau Institute, Saranac Lake, NY, USA
| | | | | | - Sean Casey
- Trudeau Institute, Saranac Lake, NY, USA
| | | | | | | | | | - Purva Vats
- The Jackson Laboratory, Farmington, CT, USA
| | | | - Isaac Bell
- The Jackson Laboratory, Farmington, CT, USA
| | - Mike Tighe
- Trudeau Institute, Saranac Lake, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Nadia A Rosenthal
- The Jackson Laboratory, Bar Harbor, ME, USA.
- National Heart and Lung Institute, Imperial College London, London, UK.
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11
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Luo M, Zhou R, Tang B, Liu H, Chen B, Liu N, Mo Y, Zhang P, Lee YL, Ip JD, Wing-Ho Chu A, Chan WM, Man HO, Chen Y, To KKW, Yuen KY, Dang S, Chen Z. Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants. EBioMedicine 2024; 108:105354. [PMID: 39341153 PMCID: PMC11470419 DOI: 10.1016/j.ebiom.2024.105354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/03/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND The spread of emerging SARS-CoV-2 immune escape sublineages, especially JN.1 and KP.2, has resulted in new waves of COVID-19 globally. The evolving memory B cell responses elicited by the parental Omicron variants to subvariants with substantial antigenic drift remain incompletely investigated. METHODS Using the single B cell antibody cloning technology, we isolated single memory B cells, delineated the B cell receptor repertoire and conducted the pseudovirus-based assay for recovered neutralizing antibodies (NAb) screening. We analyzed the cryo-EM structures of top broadly NAbs (bnAbs) and evaluated their in vivo efficacy (golden Syrian hamster model). FINDINGS By investigating the evolution of human B cell immunity, we discovered a new panel of bnAbs arising from vaccinees after Omicron BA.2/BA.5 breakthrough infections. Two lead bnAbs neutralized major Omicron subvariants including JN.1 and KP.2 with IC50 values less than 10 ng/mL, representing ultrapotent receptor binding domain (RBD)-specific class I bnAbs. They belonged to the IGHV3-53/3-66 clonotypes instead of evolving from the pre-existing vaccine-induced IGHV1-58/IGKV3-20 bnAb ZCB11. Despite sequence diversity, they targeted previously unrecognized, highly conserved conformational epitopes in the receptor binding motif (RBM) for ultrapotent ACE2 blockade. The lead bnAb ZCP3B4 not only protected the lungs of hamsters intranasally challenged with BA.5.2, BQ.1.1 and XBB.1.5 but also prevented their contact transmission. INTERPRETATION Our findings demonstrated that class I bnAbs have evolved an ultrapotent mode of action protecting against highly transmissible and broad Omicron escape variants, and their epitopes are potential targets for novel bnAbs and vaccine development. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Mengxiao Luo
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Bingjie Tang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Hang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Bohao Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Yufei Mo
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Pengfei Zhang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Ye Lim Lee
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jonathan Daniel Ip
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Allen Wing-Ho Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Wan-Mui Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Hiu-On Man
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Yuting Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong SAR, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong SAR, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China; HKUST-Shenzhen Research Institute, Nanshan, Shenzhen, 518057, People's Republic of China.
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong SAR, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China.
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12
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [PMID: 39310238 PMCID: PMC11230071 DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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13
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Su C, He J, Wang L, Hu Y, Cao J, Bai B, Qi J, Gao GF, Yang M, Wang Q. Structural characteristics of BtKY72 RBD bound to bat ACE2 reveal multiple key residues affecting ACE2 usage of sarbecoviruses. mBio 2024; 15:e0140424. [PMID: 39082798 PMCID: PMC11389363 DOI: 10.1128/mbio.01404-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 09/12/2024] Open
Abstract
Two different sarbecoviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2, have caused serious challenges to public health. Certain sarbecoviruses utilize angiotensin-converting enzyme 2 (ACE2) as their cellular receptor, whereas some do not, speculatively due to the two deletions in their receptor-binding domain (RBD). However, it remains unclear whether sarbecoviruses with one deletion in the RBD can still bind to ACE2. Here, we showed that two phylogenetically related sarbecoviruses with one deletion, BtKY72 and BM48-31, displayed a different ACE2-usage range. The cryo-electron microscopy structure of BtKY72 RBD bound to bat ACE2 identified a key residue important for the interaction between RBD and ACE2. In addition, we demonstrated that the mutations involving four types of core residues enabled the sarbecoviruses with deletion(s) to bind to human ACE2 (hACE2) and broadened the ACE2 usage of SARS-CoV-2. Our findings help predict the potential hACE2-binding ability to emerge sarbecoviruses and develop pan-sarbecovirus therapeutic agents. IMPORTANCE Many sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), possess the ability to bind to receptor angiotensin-converting enzyme 2 (ACE2) through their receptor-binding domain (RBD). However, certain sarbecoviruses with deletion(s) in the RBD lack this capability. In this study, we investigated two closely related short-deletion sarbecoviruses, BtKY72 and BM48-31, and revealed that BtKY72 exhibited a broader ACE2-binding spectrum compared to BM48-31. Structural analysis of the BtKY72 RBD-bat ACE2 complex identifies a critical residue at position 493 contributing to these differences. Furthermore, we demonstrated that the mutations involving four core residues in the RBD enabled the sarbecoviruses with deletion(s) to bind to human ACE2 and expanded the ACE2 usage spectra of SARS-CoV-2. These findings offer crucial insights for accurately predicting the potential threat of newly emerging sarbecoviruses to human health.
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Affiliation(s)
- Chao Su
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Juanhua He
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Liang Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Yu Hu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jian Cao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
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14
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Wang S, Li W, Wang Z, Yang W, Li E, Xia X, Yan F, Chiu S. Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduct Target Ther 2024; 9:223. [PMID: 39256346 PMCID: PMC11412324 DOI: 10.1038/s41392-024-01917-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/13/2024] [Accepted: 07/05/2024] [Indexed: 09/12/2024] Open
Abstract
To adequately prepare for potential hazards caused by emerging and reemerging infectious diseases, the WHO has issued a list of high-priority pathogens that are likely to cause future outbreaks and for which research and development (R&D) efforts are dedicated, known as paramount R&D blueprints. Within R&D efforts, the goal is to obtain effective prophylactic and therapeutic approaches, which depends on a comprehensive knowledge of the etiology, epidemiology, and pathogenesis of these diseases. In this process, the accessibility of animal models is a priority bottleneck because it plays a key role in bridging the gap between in-depth understanding and control efforts for infectious diseases. Here, we reviewed preclinical animal models for high priority disease in terms of their ability to simulate human infections, including both natural susceptibility models, artificially engineered models, and surrogate models. In addition, we have thoroughly reviewed the current landscape of vaccines, antibodies, and small molecule drugs, particularly hopeful candidates in the advanced stages of these infectious diseases. More importantly, focusing on global trends and novel technologies, several aspects of the prevention and control of infectious disease were discussed in detail, including but not limited to gaps in currently available animal models and medical responses, better immune correlates of protection established in animal models and humans, further understanding of disease mechanisms, and the role of artificial intelligence in guiding or supplementing the development of animal models, vaccines, and drugs. Overall, this review described pioneering approaches and sophisticated techniques involved in the study of the epidemiology, pathogenesis, prevention, and clinical theatment of WHO high-priority pathogens and proposed potential directions. Technological advances in these aspects would consolidate the line of defense, thus ensuring a timely response to WHO high priority pathogens.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Wujian Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhenshan Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin, China
| | - Wanying Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China.
- Department of Laboratory Medicine, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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15
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Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JPM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Jain S, Wali B, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Suthar MS, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC. Variant-proof high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. Nat Commun 2024; 15:6894. [PMID: 39134521 PMCID: PMC11319446 DOI: 10.1038/s41467-024-51046-w] [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: 11/21/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
SARS-CoV-2 has the capacity to evolve mutations that escape vaccine- and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool that would maintain its efficacy despite the ongoing emergence of new variants. Here, we challenge male rhesus macaques with SARS-CoV-2 Delta-the most pathogenic variant in a highly susceptible animal model. At the time of challenge, we also treat the macaques with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment equivalently suppresses virus replication in both upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 does not block the development of virus-specific T- and B-cell responses and does not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
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Affiliation(s)
- Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barbara J Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Cole Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dillon R Flebbe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shayne F Andrew
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samantha J Provost
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Fred Hutch Cancer Center, Seattle, WA, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saran Bao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Chunlin Li
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shilpi Jain
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Bushra Wali
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | | | | | | | | | | | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines, Children's Healthcare of Atlanta, Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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16
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Xu J, Gong J, Bo X, Tong Y, Ren Z, Ni M. A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity. Biophys Chem 2024; 311:107253. [PMID: 38768531 DOI: 10.1016/j.bpc.2024.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/08/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between -0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.
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Affiliation(s)
- Jiayi Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jianting Gong
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zilin Ren
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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17
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Baker CN, Duso D, Kothapalli N, Hart T, Casey S, Cookenham T, Kummer L, Hvizdos J, Lanzer K, Vats P, Shanbhag P, Bell I, Tighe M, Travis K, Szaba F, Bedard O, Oberding N, Ward JM, Adams MD, Lutz C, Bradrick SS, Reiley WW, Rosenthal N. Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19. RESEARCH SQUARE 2024:rs.3.rs-4675061. [PMID: 39149485 PMCID: PMC11326417 DOI: 10.21203/rs.3.rs-4675061/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a limited range of other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad range of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.
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18
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Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X. An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep 2024; 43:114265. [PMID: 38805396 DOI: 10.1016/j.celrep.2024.114265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.
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Affiliation(s)
- Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yijun Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qian Wang
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China
| | - Yuanyi Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Shuangshuang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingxian Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengzhen Su
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Xiancheng Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Science and Technology of China, Hefei, China
| | - Yinglin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyi Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Ling Chen
- Guangzhou Laboratory & Bioland Laboratory, Guangzhou, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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19
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Iglesias-Caballero M, Mas V, Vázquez-Morón S, Vázquez M, Camarero-Serrano S, Cano O, Palomo C, Ruano MJ, Cano-Gómez C, Infantes-Lorenzo JA, Campoy A, Agüero M, Pozo F, Casas I. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. Int J Mol Sci 2024; 25:5499. [PMID: 38791536 PMCID: PMC11122236 DOI: 10.3390/ijms25105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.
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Affiliation(s)
- María Iglesias-Caballero
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Vicente Mas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sonia Vázquez-Morón
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mónica Vázquez
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sara Camarero-Serrano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Olga Cano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Concepción Palomo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - María José Ruano
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Cristina Cano-Gómez
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - José Antonio Infantes-Lorenzo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Albert Campoy
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Montserrat Agüero
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Francisco Pozo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Inmaculada Casas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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20
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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21
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Scovino AM, Dahab EC, Diniz-Lima I, de Senna Silveira E, Barroso SPC, Cardoso KM, Nico D, Makhoul GJ, da Silva-Junior EB, Freire-de-Lima CG, Freire-de-Lima L, da Fonseca LM, Valente N, Nacife V, Machado A, Araújo M, Vieira GF, Pauvolid-Corrêa A, Siqueira M, Morrot A. A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants. Microorganisms 2024; 12:720. [PMID: 38674664 PMCID: PMC11052025 DOI: 10.3390/microorganisms12040720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 04/28/2024] Open
Abstract
The SARS-CoV-2 P.1 variant, responsible for an outbreak in Manaus, Brazil, is distinguished by 12 amino acid differences in the S protein, potentially increasing its ACE-2 affinity and immune evasion capability. We investigated the innate immune response of this variant compared to the original B.1 strain, particularly concerning cytokine production. Blood samples from three severe COVID-19 patients were analyzed post-infection with both strains. Results showed no significant difference in cytokine production of mononuclear cells and neutrophils for either variant. While B.1 had higher cytopathogenicity, neither showed viral replication in mononuclear cells. Structural analyses of the S protein highlighted physicochemical variations, which might be linked to the differences in infectivity between the strains. Our studies point to the increased infectivity of P.1 could stem from altered immunogenicity and receptor-binding affinity.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Israel Diniz-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Etiele de Senna Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
| | - Shana Priscila Coutinho Barroso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
- Biomanguinhos, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, Brazil
| | - Karina Martins Cardoso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
| | - Dirlei Nico
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
| | - Gustavo José Makhoul
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Elias Barbosa da Silva-Junior
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
- Curso de Medicina, Universidade Castelo Branco (UCB), Rio de Janeiro 21710-255, Brazil
| | - Natalia Valente
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Valeria Nacife
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Ana Machado
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Mia Araújo
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Gustavo Fioravanti Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
- PPGSDH—Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas 92010-000, Brazil
| | - Alex Pauvolid-Corrêa
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Laboratório de Virologia Veterinária de Viçosa, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Marilda Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Alexandre Morrot
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
- Escola de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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22
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Meng H, Wang Y, Zhai Y, Luo W, Wang Y, Hu Y, Liu S, Xiao W, Yang G, Ye F, Chen S, Jie Y, Chen YQ. Unveiling the micronutrient-immunity puzzle in inactivated COVID-19 vaccination: A comprehensive analysis of circulating micronutrient levels and humoral responses in healthy adults. J Med Virol 2024; 96:e29611. [PMID: 38639305 DOI: 10.1002/jmv.29611] [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: 01/30/2024] [Revised: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
While micronutrients are crucial for immune function, their impact on humoral responses to inactivated COVID-19 vaccination remains unclear. We investigated the associations between seven key micronutrients and antibody responses in 44 healthy adults with two doses of an inactivated COVID-19 vaccine. Blood samples were collected pre-vaccination and 28 days post-booster. We measured circulating minerals (iron, zinc, copper, and selenium) and vitamins (A, D, and E) concentrations alongside antibody responses and assessed their associations using linear regression analyses. Our analysis revealed inverse associations between blood iron and zinc concentrations and anti-SARS-CoV-2 IgM antibody binding affinity (AUC for iron: β = -258.21, p < 0.0001; zinc: β = -17.25, p = 0.0004). Notably, antibody quality presented complex relationships. Blood selenium was positively associated (β = 18.61, p = 0.0030), while copper/selenium ratio was inversely associated (β = -1.36, p = 0.0055) with the neutralizing ability against SARS-CoV-2 virus at a 1:10 plasma dilution. There was no significant association between circulating micronutrient concentrations and anti-SARS-CoV-2 IgG binding affinity. These findings suggest that circulating iron, zinc, and selenium concentrations and copper/selenium ratio, may serve as potential biomarkers for both quantity (binding affinity) and quality (neutralization) of humoral responses after inactivated COVID-19 vaccination. Furthermore, they hint at the potential of pre-vaccination dietary interventions, such as selenium supplementation, to improve vaccine efficacy. However, larger, diverse studies are needed to validate these findings. This research advances the understanding of the impact of micronutrients on vaccine response, offering the potential for personalized vaccination strategies.
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Affiliation(s)
- Huicui Meng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Yin Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Yanmei Zhai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Wanyu Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Sizhe Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
| | - Weimin Xiao
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, China
| | - Guowu Yang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, China
| | - Feng Ye
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Shifeng Chen
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Yusheng Jie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Guangdong, Shenzhen, China
- Ministry of Education, Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Guangzhou, China
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23
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Guo XL, Wang K, Jin J, Dai LL. Efficacy of the combination of BRII-196/BRII-198 in the treatment of COVID-19 vaccine breakthrough infections. Am J Transl Res 2024; 16:916-924. [PMID: 38586111 PMCID: PMC10994788 DOI: 10.62347/ndgv1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND BRII-196 and BRII-198 are two recombinant human immunoglobulin (Ig) G1 monoclonal antibodies (mAbs) that non-competitively target distinct epitope regions within the receptor-binding domain (RBD) of the coronavirus spike glycoproteins. These antibodies are derived directly from human B cells of individuals who recovered from COVID-19. OBJECTIVE To analyze the efficacy of BRII-196/BRII-198 in the treatment of coronavirus disease 2019 (COVID-19) vaccine breakthrough infections. METHODS COVID-19 patients at high risk of progressing to severe and critical illness, with an initial SARS-CoV-2 immunoglobulin (Ig) G antibody level < 1.0 S/CO (detected within 24-48 hours post COVID-19 diagnosis), were treated with BRII-196/BRII-198 within three days of symptom onset. Treatment continued until the antibody level exceeded 1.0 S/CO. Patients whose absolute lymphocyte count (ALC) at first detection (within 24-48 h post-diagnosis) was < 0.8 × 109/L received thymalfasin therapy within three days of symptom onset, continuing until the ALC level surpassed 0.8 × 109/L. We determined the correlation of SARS-CoV-2 IgG antibody level and ALC with the condition of COVID-19 patients. Additionally, we analyzed the effects of BRII-196/BRII-198 on SARS-CoV-2 nucleic acid (NA) negative conversion, lymphocyte count recovery, and the change in SARS-CoV-2 IgG antibody level from the first positive NA test for SARS-CoV-2 to negative conversion in COVID-19 patients. RESULTS A total of 61 cases of breakthrough infections were observed, classified as 10 mild cases, 31 ordinary cases, and 20 severe cases. Among these, 20%, 48.4% and 75% of the patients with mild, ordinary, and severe COVID-19, respectively, had initial SARS-CoV-2 IgG antibody level < 1.0 S/CO. Additionally, 0%, 35% and 70% had initial ALC < 0.8 × 109/L, respectively. Fifteen ordinary and 15 severe COVID-19 patients were treated with BRII-196/BRII-198. In severely infected patients, BRII-196/BRII-198 treatment showed statistically significant differences in NA negative conversion time and changes in SARS-CoV-2 IgG antibody levels (P < 0.05). However, in patients classified with ordinary severity, BRII-196/BRII-198 treatment did not lead to notable differences in NA negative conversion time or changes in SARS-CoV-2 IgG antibody level (P > 0.05). BRII-196/BRII-198 therapy was not associated with lymphocyte count recovery time in patients with either ordinary and/or severe COVID-19 (P > 0.05). CONCLUSIONS The initial levels of SARS-CoV-2 IgG antibody and lymphocytes in fully vaccinated patients with breakthrough infections are inversely correlated with the severity of the disease. Early treatment with BRII-196/BRII-198 can shorten NA negative conversion time in severe COVID-19 patients and increase in vivo neutralizing antibody levels post-conversion, providing lasting protection. However, BRII-196/BRII-198 does not influence lymphocyte count recovery in patients with either ordinary and/or severe COVID-19.
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Affiliation(s)
- Xiao-Ling Guo
- Department of Respiratory Medicine, Pulmonary Hospital of LanzhouLanzhou 730046, Gansu, China
| | - Kun Wang
- Department of Respiratory Medicine, Pulmonary Hospital of LanzhouLanzhou 730046, Gansu, China
| | - Jie Jin
- Department of Respiratory Medicine, Pulmonary Hospital of LanzhouLanzhou 730046, Gansu, China
| | - Li-Li Dai
- Center for Diagnosis and Treatment of Infectious Diseases, Beijing You An Hospital, Capital Medical UniversityBeijing 100069, China
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24
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Yu P, Ran J, Yang R, Zhu H, Lu S, Wu Y, Zhao T, Xiong T. Rapid isolation of pan-neutralizing antibodies against Omicron variants from convalescent individuals infected with SARS-CoV-2. Front Immunol 2024; 15:1374913. [PMID: 38510237 PMCID: PMC10950932 DOI: 10.3389/fimmu.2024.1374913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction The emergence of SARS-CoV-2 Omicron subvariants has presented a significant challenge to global health, as these variants show resistance to most antibodies developed early in the pandemic. Therapeutic antibodies with potent efficacy to the Omicron variants are urgently demanded. Methods Utilizing the rapid antibody discovery platform, Berkeley Lights Beacon, we isolated two monoclonal neutralizing antibodies, 2173-A6 and 3462-A4. These antibodies were isolated from individuals who recently recovered from Omicron infections. Results Both antibodies, 2173-A6 and 3462-A4, demonstrated high affinity for the RBD and effectively neutralized pseudoviruses from various Omicron lineages, including BA.4/5, XBB.1.16, XBB.1.5, and EG.5.1. This neutralization was achieved through binding to identical or overlapping epitopes. Discussion The use of the Beacon platform enabled the rapid isolation and identification of effective neutralizing antibodies within less than 10 days. This process significantly accelerates the development of novel therapeutic antibodies, potentially reducing the time required to respond to unknown infectious diseases in the future.
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Affiliation(s)
- Peng Yu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Jingping Ran
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Ruiqi Yang
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Hang Zhu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Song Lu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Yuzhang Wu
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
| | - Tingting Zhao
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Tianchen Xiong
- Antibody Research Platform, Chongqing International Institute for Immunology, Chongqing, China
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25
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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26
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Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM. Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166959. [PMID: 37967796 DOI: 10.1016/j.bbadis.2023.166959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
COVID-19 has resulted in millions of deaths and severe impact on economies worldwide. Moreover, the emergence of SARS-CoV-2 variants presented significant challenges in controlling the pandemic, particularly their potential to avoid the immune system and evade vaccine immunity. This has led to a growing need for research to predict how mutations in SARS-CoV-2 reduces the ability of antibodies to neutralize the virus. In this study, we assembled a set of 1813 mutations from the interface of SARS-CoV-2 spike protein's receptor binding domain (RBD) and neutralizing antibody complexes and developed a machine learning model to classify high or low escape mutations using interaction energy, inter-residue contacts and predicted binding free energy change. Our approach achieved an Area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.91 using the Random Forest classifier on the test dataset with 217 mutations. The model was further utilized to predict the escape mutations on a dataset of 29,165 mutations located at the interface of 83 RBD-neutralizing antibody complexes. A small subset of this dataset was also validated based on available experimental data. We found that top 10 % high escape mutations were dominated by charged to nonpolar mutations whereas low escape mutations were dominated by polar to nonpolar mutations. We believe that the present method will allow prioritization of high/low escape mutations in the context of neutralizing antibodies targeting SARS-CoV-2 RBD region and assist antibody design for current and emerging variants.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Puneet Rawat
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
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27
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Cani M, Epistolio S, Dazio G, Modesti M, Salfi G, Pedrani M, Isella L, Gillessen S, Vogl UM, Tortola L, Treglia G, Buttigliero C, Frattini M, Pereira Mestre R. Antiandrogens as Therapies for COVID-19: A Systematic Review. Cancers (Basel) 2024; 16:298. [PMID: 38254788 PMCID: PMC10814161 DOI: 10.3390/cancers16020298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND In 2019, the breakthrough of the coronavirus 2 disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represented one of the major issues of our recent history. Different drugs have been tested to rapidly find effective anti-viral treatments and, among these, antiandrogens have been suggested to play a role in mediating SARS-CoV-2 infection. Considering the high heterogeneity of studies on this topic, we decided to review the current literature. METHODS We performed a systematic review according to PRISMA guidelines. A search strategy was conducted on PUBMED and Medline. Only original articles published from March 2020 to 31 August 2023 investigating the possible protective role of antiandrogens were included. In vitro or preclinical studies and reports not in the English language were excluded. The main objective was to investigate how antiandrogens may interfere with COVID-19 outcomes. RESULTS Among 1755 records, we selected 31 studies, the majority of which consisted of retrospective clinical data collections and of randomized clinical trials during the first and second wave of the COVID-19 pandemic. CONCLUSIONS In conclusion, we can state that antiandrogens do not seem to protect individuals from SARS-CoV-2 infection and COVID-19 severity and, thus, their use should not be encouraged in this field.
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Affiliation(s)
- Massimiliano Cani
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Oncology Unit, Department of Oncology, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Italy;
| | - Samantha Epistolio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Giulia Dazio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Mikol Modesti
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Giuseppe Salfi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland
| | - Martino Pedrani
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Luca Isella
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Silke Gillessen
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
| | - Ursula Maria Vogl
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Luigi Tortola
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Giorgio Treglia
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
- Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, 1005 Lausanne, Switzerland
| | - Consuelo Buttigliero
- Oncology Unit, Department of Oncology, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Italy;
| | - Milo Frattini
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Ricardo Pereira Mestre
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
- Clinical Research Unit, myDoctorAngel, 6934 Bioggio, Switzerland
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28
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Wang Y, Hu Y, Ma Y, Li P, Zhou S, Xu M, He B, Liu S, Lv K, Liu S, Zhang Y, Zhou N, Chen S, Ye F, Chen YQ. RBD class 1 and 2 antibody epitopes elicit around 70% neutralizing capacity against SARS-CoV-2 virus following boosting with inactivated virus vaccine. Vaccine 2023; 41:7641-7646. [PMID: 38016845 DOI: 10.1016/j.vaccine.2023.11.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/13/2023] [Accepted: 11/18/2023] [Indexed: 11/30/2023]
Abstract
A third dose of inactivated virus vaccine (IVV) boosts neutralizing antibodies, reducing SARS-CoV-2 transmission rate and COVID-19 severity. However, the impact of RBD-elicited antibodies and their neutralizing activity by the boost of IVV is unknown. We investigated the impact of IVV's boost shot on RBD-elicited antibodies and their neutralizing activity in 18 subjects receiving the second and third IVV doses. Using an RBD antibodies depletion assay, we assessed the neutralizing activity of RBD-elicited antibodies. After the second dose, RBD-antigen elicitation accounted for ∼60% of neutralizing activity, which increased to 82% after the IVV boost against ancestral SARS-CoV-2. Depleting class 3 and class 4-specific antibodies with the Beta-RBD protein revealed that NAbs targeting RBD class 1 and class 2 subdomains increased from 57% to 75% post-boost. These findings highlight the significant enhancement of RBD-specific antibodies, especially against RBD class 1 and class 2, with IVV booster doses. Our study offers valuable insights for optimizing COVID-19 vaccine strategies.
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Affiliation(s)
- Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yong Ma
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pengbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Siwei Zhou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Bing He
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Sizhe Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yu Zhang
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Na Zhou
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Shifeng Chen
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Feng Ye
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China; National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Sun Yat-sen University, Guanzhou, China.
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29
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Zaidi AK, Bajpai S, Dehgani-Mobaraki P. B cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 202:155-181. [PMID: 38237985 DOI: 10.1016/bs.pmbts.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides an overview of B cell responses in COVID-19, highlighting the structure of SARS-CoV-2 and its impact on B cell immunity. It explores the production and maturation of SARS-CoV-2-specific B cells, with a focus on the two distinct phases of the humoral immune response: the extrafollicular (EF) phase and the germinal center (GC) phase. Furthermore, the interplay between B cells, follicular T helper cells, CD4+ T cells, and plasma cells is discussed, emphasizing their collaborative role in mounting an effective humoral immune response against SARS-CoV-2. The concept of immunological memory is explored, highlighting the roles of plasma cells and B memory cells in providing long-term protection. The chapter delves into the antibody response during SARS-CoV-2 infection, categorizing the types of antibodies generated. This includes a detailed analysis of neutralizing antibodies, such as those directed against the receptor-binding domain (RBD) and the N-terminal domain (NTD), as well as non-neutralizing antibodies. The role of mucosal antibodies, cross-reactive antibodies, and auto-reactive antibodies is also discussed. Factors influencing the dynamics of anti-SARS-CoV-2 antibodies are examined, including the duration and strength of the humoral response. Additionally, the chapter highlights the impact of the Omicron variant on humoral immune responses and its implications for vaccine efficacy and antibody-mediated protection.
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Affiliation(s)
| | - Sanchit Bajpai
- Consultant ENT & Head and Neck Surgeon at TSM Medical College and Multispeciality Hospital, Lucknow, India.
| | - Puya Dehgani-Mobaraki
- Founder and President, Associazione Naso Sano, Ringgold Institution ID 567754, San Mariano, Italy
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30
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Hilligan KL, Namasivayam S, Clancy CS, Baker PJ, Old SI, Peluf V, Amaral EP, Oland SD, O'Mard D, Laux J, Cohen M, Garza NL, Lafont BAP, Johnson RF, Feng CG, Jankovic D, Lamiable O, Mayer-Barber KD, Sher A. Bacterial-induced or passively administered interferon gamma conditions the lung for early control of SARS-CoV-2. Nat Commun 2023; 14:8229. [PMID: 38086794 PMCID: PMC10716133 DOI: 10.1038/s41467-023-43447-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Type-1 and type-3 interferons (IFNs) are important for control of viral replication; however, less is known about the role of Type-2 IFN (IFNγ) in anti-viral immunity. We previously observed that lung infection with Mycobacterium bovis BCG achieved though intravenous (iv) administration provides strong protection against SARS-CoV-2 in mice yet drives low levels of type-1 IFNs but robust IFNγ. Here we examine the role of ongoing IFNγ responses to pre-established bacterial infection on SARS-CoV-2 disease outcomes in two murine models. We report that IFNγ is required for iv BCG induced reduction in pulmonary viral loads, an outcome dependent on IFNγ receptor expression by non-hematopoietic cells. Importantly, we show that BCG infection prompts pulmonary epithelial cells to upregulate IFN-stimulated genes with reported anti-viral activity in an IFNγ-dependent manner, suggesting a possible mechanism for the observed protection. Finally, we confirm the anti-viral properties of IFNγ by demonstrating that the recombinant cytokine itself provides strong protection against SARS-CoV-2 challenge when administered intranasally. Together, our data show that a pre-established IFNγ response within the lung is protective against SARS-CoV-2 infection, suggesting that concurrent or recent infections that drive IFNγ may limit the pathogenesis of SARS-CoV-2 and supporting possible prophylactic uses of IFNγ in COVID-19 management.
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Affiliation(s)
- Kerry L Hilligan
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
- Malaghan Institute of Medical Research, Wellington, 6012, New Zealand.
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Paul J Baker
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel I Old
- Malaghan Institute of Medical Research, Wellington, 6012, New Zealand
| | - Victoria Peluf
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eduardo P Amaral
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sandra D Oland
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Danielle O'Mard
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julie Laux
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicole L Garza
- SARS-CoV2- Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bernard A P Lafont
- SARS-CoV2- Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Reed F Johnson
- SARS-CoV2- Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Carl G Feng
- Immunology and Host Defense Group, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
- Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Dragana Jankovic
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olivier Lamiable
- Malaghan Institute of Medical Research, Wellington, 6012, New Zealand
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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31
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Zhang Q, Yang Y, Lan J, Wang Z, Gao Y, Li X, Mao W, Xie J, Mi LZ, Zhang X, Wang X, Mu X, Mei K. Inducing enhanced neutralizing antibodies against broad SARS-CoV-2 variants through glycan-shielding multiple non-neutralizing epitopes of RBD. Front Immunol 2023; 14:1259386. [PMID: 38149245 PMCID: PMC10750354 DOI: 10.3389/fimmu.2023.1259386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Since the outbreak of SARS-CoV-2, vaccines have demonstrated their effectiveness in resisting virus infection, reducing severity, and lowering the mortality rate in infected individuals. However, due to the rapid and ongoing mutations of SARS-CoV-2, the protective ability of many available vaccines has been challenged. Therefore, there is an urgent need for vaccines capable of eliciting potent broadly neutralizing antibodies against various SARS-CoV-2 variants. Methods In this study, we developed a novel subunit vaccine candidate for SARS-CoV-2 by introducing a series of shielding glycans to the Fc-fused receptor-binding domain (RBD) of the prototypic spike protein. This approach aims to mask non-neutralizing epitopes and focus the immune response on crucial neutralizing epitopes. Results All modified sites were confirmed to be highly glycosylated through mass spectrometry analysis. The binding affinity of the glycan-shielded RBD (gsRBD) to the human ACE2 receptor was comparable to that of the wildtype RBD (wtRBD). Immunizing mice with gsRBD when combined with either Freund's adjuvant or aluminum adjuvant demonstrated that the introduction of the glycan shield did not compromise the antibody-inducing ability of RBD. Importantly, the gsRBD significantly enhanced the generation of neutralizing antibodies against SARS-CoV-2 pseudoviruses compared to the wtRBD. Notably, it exhibited remarkable protective activity against Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), approximately 3-fold, 7- fold, and 17-fold higher than wtRBD, respectively. Discussion Our data proved this multiple-epitope masking strategy as an effective approach for highly active vaccine production.
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Affiliation(s)
- Qingyun Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Jun Lan
- School of Life Sciences, Tsinghua University, Beijing, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Ziyi Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xiao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Weidong Mao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinquan Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
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32
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Zhang Y, Zhao Y, Liang H, Xu Y, Zhou C, Yao Y, Wang H, Yang X. Innovation-driven trend shaping COVID-19 vaccine development in China. Front Med 2023; 17:1096-1116. [PMID: 38102402 DOI: 10.1007/s11684-023-1034-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 12/17/2023]
Abstract
Confronted with the Coronavirus disease 2019 (COVID-19) pandemic, China has become an asset in tackling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and mutation, with several innovative platforms, which provides various technical means in this persisting combat. Derived from collaborated researches, vaccines based on the spike protein of SARS-CoV-2 or inactivated whole virus are a cornerstone of the public health response to COVID-19. Herein, we outline representative vaccines in multiple routes, while the merits and plights of the existing vaccine strategies are also summarized. Likewise, new technologies may provide more potent or broader immunity and will contribute to fight against hypermutated SARS-CoV-2 variants. All in all, with the ultimate aim of delivering robust and durable protection that is resilient to emerging infectious disease, alongside the traditional routes, the discovery of innovative approach to developing effective vaccines based on virus properties remains our top priority.
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Affiliation(s)
- Yuntao Zhang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuxiu Zhao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hongyang Liang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Ying Xu
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Chuge Zhou
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuzhu Yao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hui Wang
- China National Biotec Group Company Limited, Beijing, 100029, China.
| | - Xiaoming Yang
- China National Biotec Group Company Limited, Beijing, 100029, China.
- National Engineering Technology Research Center of Combined Vaccines, Wuhan, 430207, China.
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33
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Zhou B, Zhou R, Chan JFW, Zeng J, Zhang Q, Yuan S, Liu L, Robinot R, Shan S, Liu N, Ge J, Kwong HYH, Zhou D, Xu H, Chan CCS, Poon VKM, Chu H, Yue M, Kwan KY, Chan CY, Chan CCY, Chik KKH, Du Z, Au KK, Huang H, Man HO, Cao J, Li C, Wang Z, Zhou J, Song Y, Yeung ML, To KKW, Ho DD, Chakrabarti LA, Wang X, Zhang L, Yuen KY, Chen Z. SARS-CoV-2 hijacks neutralizing dimeric IgA for nasal infection and injury in Syrian hamsters 1. Emerg Microbes Infect 2023; 12:2245921. [PMID: 37542391 PMCID: PMC10444022 DOI: 10.1080/22221751.2023.2245921] [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: 04/24/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
Prevention of robust severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in nasal turbinate (NT) requires in vivo evaluation of IgA neutralizing antibodies. Here, we report the efficacy of receptor binding domain (RBD)-specific monomeric B8-mIgA1 and B8-mIgA2, and dimeric B8-dIgA1, B8-dIgA2 and TH335-dIgA1 against intranasal SARS-CoV-2 challenge in Syrian hamsters. These antibodies exhibited comparable neutralization potency against authentic virus by competing with human angiotensin converting enzyme-2 (ACE2) receptor for RBD binding. While reducing viral loads in lungs significantly, prophylactic intranasal B8-dIgA unexpectedly led to high amount of infectious viruses and extended damage in NT compared to controls. Mechanistically, B8-dIgA failed to inhibit SARS-CoV-2 cell-to-cell transmission, but was hijacked by the virus through dendritic cell-mediated trans-infection of NT epithelia leading to robust nasal infection. Cryo-EM further revealed B8 as a class II antibody binding trimeric RBDs in 3-up or 2-up/1-down conformation. Neutralizing dIgA, therefore, may engage an unexpected mode of SARS-CoV-2 nasal infection and injury.
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Affiliation(s)
- Biao Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianwei Zeng
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Qi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Shuofeng Yuan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Li Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Rémy Robinot
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Hugo Yat-Hei Kwong
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Dongyan Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haoran Xu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chung-Sing Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hin Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Ming Yue
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Yi Kwan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chun-Yin Chan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Kenn Ka-Heng Chik
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhenglong Du
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Kit Au
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haode Huang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hiu-On Man
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianli Cao
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Cun Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jie Zhou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Youqiang Song
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Man-Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lisa A. Chakrabarti
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
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Katzmarzyk M, Clesle DC, van den Heuvel J, Hoffmann M, Garritsen H, Pöhlmann S, Jacobsen H, Čičin-Šain L. Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera. Front Immunol 2023; 14:1288794. [PMID: 38022629 PMCID: PMC10667444 DOI: 10.3389/fimmu.2023.1288794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The evolution of novel SARS-CoV-2 variants significantly affects vaccine effectiveness. While these effects can only be studied retrospectively, neutralizing antibody titers are most used as correlates of protection. However, studies assessing neutralizing antibody titers often show heterogeneous data. Methods To address this, we investigated assay variance and identified virus infection time and dose as factors affecting assay robustness. We next measured neutralization against Omicron sub-variants in cohorts with hybrid or vaccine induced immunity, identifying a gradient of immune escape potential. To evaluate the effect of individual mutations on this immune escape potential of Omicron variants, we systematically assessed the effect of each individual mutation specific to Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5. Results We cloned a library of pseudo-viruses expressing spikes with single point mutations, and subjected it to pooled sera from vaccinated hosts, thereby identifying multiple mutations that independently affect neutralization potency. Discussion These data might help to predict antigenic features of novel viral variants carrying these mutations and support the development of broad monoclonal antibodies.
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Affiliation(s)
- Maeva Katzmarzyk
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Denise Christine Clesle
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Research Group Recombinant Protein Expression, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Henk Garritsen
- Institute for Clinical Transfusion Medicine, Klinikum Braunschweig GmbH, Braunschweig, Germany
- Fraunhofer Institute for Surface Engineering and Thin Films IST, Braunschweig, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CIIM), Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, Braunschweig, Germany
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35
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Focosi D, McConnell S, Sullivan DJ, Casadevall A. Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment. Drug Resist Updat 2023; 71:100991. [PMID: 37572569 DOI: 10.1016/j.drup.2023.100991] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/14/2023]
Abstract
The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 32 publications detailing 216 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesn't allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Italy.
| | - Scott McConnell
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David J Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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36
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Yasugi M, Nakagama Y, Kaku N, Nitahara Y, Hatanaka N, Yamasaki S, Kido Y. Characteristics of epitope dominance pattern and cross-variant neutralisation in 16 SARS-CoV-2 mRNA vaccine sera. Vaccine 2023; 41:6248-6254. [PMID: 37673717 DOI: 10.1016/j.vaccine.2023.08.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 serological studies suggest that individual serum antibody repertoires can affect neutralisation breadth. Herein, we asked whether a BNT162b2 vaccine-induced epitope dominance pattern (i.e., predominant viral structural domain targeted by serum antibodies for virus neutralisation) affects cross-variant neutralisation. When a neutralisation assay against the ancestral strain was carried out using 16 vaccine sera preabsorbed with a recombinant receptor-binding domain (RBD) or an N-terminal domain (NTD) protein, three and 13 sera, respectively, showed lower neutralisation under NTD and RBD protein-preabsorbed conditions than under the other protein-preabsorbed conditions. This suggests that the NTD was responsible for virus neutralisation in three sera, whereas the other 13 sera elicited RBD-dominant neutralisation. The results also suggest the presence of infectivity-enhancing antibodies in four out of the 13 RBD-dominant sera. A neutralisation assay using SARS-CoV-2 variants revealed that NTD-dominant sera showed significantly reduced neutralising activity against the B.1.617.2 variant, whereas RBD-dominant sera retained neutralising activity even in the presence of infectivity-enhancing antibodies. Taken together, these results suggest the followings: (i) epitope dominance patterns are divided into at least two types: NTD-dominant and RBD-dominant; (ii) NTD-dominant sera have less potential to neutralise the B.1.617.2 variant than RBD-dominant sera; and (iii) infectivity-enhancing antibodies play a limited role in cross-variant neutralisation against the five variants tested.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan.
| | - Yu Nakagama
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natsuko Kaku
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Noritoshi Hatanaka
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Yasutoshi Kido
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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37
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Chakraborty S, Saha C. A multi-tier computational screening framework to effectively search the mutational space of SARS-CoV-2 receptor binding motif to identify mutants with enhanced ACE2 binding abilities. Mol Inform 2023; 42:e2300055. [PMID: 37590498 DOI: 10.1002/minf.202300055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
Abstract
SARS-CoV-2 gained crucial mutations at the receptor binding domain (RBD) that often changed the course of the pandemic leading to new waves with increased case fatality. Variants are observed with enhanced transmission and immune invasion abilities. Thus, predicting future variants with enhanced transmission ability is a problem of utmost research interest. Here, we have developed a multi-tier exhaustive SARS-CoV-2 mutation screening platform combining MM/GBSA, extensive molecular dynamics simulations, and steered molecular dynamics to identify RBD mutants with enhanced ACE2 binding capability. We have identified four RBM mutations (F490K, S494K, G504F, and the P499L) with significantly higher ACE2 binding abilities than wild-type RBD. Compared to wild-type RBD, they all form stable complexes with more hydrogen bonds and salt-bridge interactions with ACE2. Our simulation data suggest that these mutations allosterically alter the packing of the RBM interface of the RBD-ACE2 complex. As a result, the rupture force required to break the RBD-ACE2 contacts is significantly higher for these mutants.
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Affiliation(s)
- Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
| | - Chiranjeet Saha
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
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38
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Kosenko M, Onkhonova G, Susloparov I, Ryzhikov A. SARS-CoV-2 proteins structural studies using synchrotron radiation. Biophys Rev 2023; 15:1185-1194. [PMID: 37974992 PMCID: PMC10643813 DOI: 10.1007/s12551-023-01153-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.
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Affiliation(s)
- Maksim Kosenko
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Galina Onkhonova
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Ivan Susloparov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Alexander Ryzhikov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
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Thakkar R, Agarwal DK, Ranaweera CB, Ishiguro S, Conda-Sheridan M, Gaudreault NN, Richt JA, Tamura M, Comer J. De novo design of a stapled peptide targeting SARS-CoV-2 spike protein receptor-binding domain. RSC Med Chem 2023; 14:1722-1733. [PMID: 37731704 PMCID: PMC10507807 DOI: 10.1039/d3md00222e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/12/2023] [Indexed: 09/22/2023] Open
Abstract
Although effective vaccines have been developed against SARS-CoV-2, many regions in the world still have low rates of vaccination and new variants with mutations in the viral spike protein have reduced the effectiveness of most available vaccines and treatments. There is an urgent need for a drug to cure this disease and prevent infection. The SARS-CoV-2 virus enters the host cell through protein-protein interaction between the virus's spike protein and the host's angiotensin converting enzyme (ACE2). Using protein design software and molecular dynamics simulations, we have designed a 17-residue peptide (pep39), that binds to the spike protein receptor-binding domain (RBD) and blocks interaction of spike protein with ACE2. We have confirmed the binding activity of the designed peptide for the original spike protein and the delta variant spike protein using micro-cantilever and bio-layer interferometry (BLI) based methods. We also confirmed that pep39 strongly inhibits SARS-CoV-2 virus replication in Vero E6 cells. Taken together these data suggest that a newly designed spike protein RBD blocking peptide pep39 has a potential as a SARS-CoV-2 virus inhibitor.
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Affiliation(s)
- Ravindra Thakkar
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Dilip K Agarwal
- Department of Material Science and Engineering and NUANCE Center, Northwestern University Evanston Illinois USA
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, General Sir John Kotelawala Defense University Colombo Sri Lanka
| | - Susumu Ishiguro
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha Nebraska USA
| | - Natasha N Gaudreault
- Department of Diagnostic Medicine & Pathobiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Juergen A Richt
- Department of Diagnostic Medicine & Pathobiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Masaaki Tamura
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Jeffrey Comer
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
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40
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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41
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Qing E, Gallagher T. Adaptive variations in SARS-CoV-2 spike proteins: effects on distinct virus-cell entry stages. mBio 2023; 14:e0017123. [PMID: 37382441 PMCID: PMC10470846 DOI: 10.1128/mbio.00171-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/14/2023] [Indexed: 06/30/2023] Open
Abstract
Evolved SARS-CoV-2 variants of concern (VOCs) spread through human populations in succession. Major virus variations are in the entry-facilitating viral spike (S) proteins; Omicron VOCs have 29-40 S mutations relative to ancestral D614G viruses. The impacts of this Omicron divergence on S protein structure, antigenicity, cell entry pathways, and pathogenicity have been extensively evaluated, yet gaps remain in correlating specific alterations with S protein functions. In this study, we compared the functions of ancestral D614G and Omicron VOCs using cell-free assays that can reveal differences in several distinct steps of the S-directed virus entry process. Relative to ancestral D614G, Omicron BA.1 S proteins were hypersensitized to receptor activation, to conversion into intermediate conformational states, and to membrane fusion-activating proteases. We identified mutations conferring these changes in S protein character by evaluating domain-exchanged D614G/Omicron recombinants in the cell-free assays. Each of the three functional alterations was mapped to specific S protein domains, with the recombinants providing insights on inter-domain interactions that fine-tune S-directed virus entry. Our results provide a structure-function atlas of the S protein variations that may promote the transmissibility and infectivity of current and future SARS-CoV-2 VOCs. IMPORTANCE Continuous SARS-CoV-2 adaptations generate increasingly transmissible variants. These succeeding variants show ever-increasing evasion of suppressive antibodies and host factors, as well as increasing invasion of susceptible host cells. Here, we evaluated the adaptations enhancing invasion. We used reductionist cell-free assays to compare the entry steps of ancestral (D614G) and Omicron (BA.1) variants. Relative to D614G, Omicron entry was distinguished by heightened responsiveness to entry-facilitating receptors and proteases and by enhanced formation of intermediate states that execute virus-cell membrane fusion. We found that these Omicron-specific characteristics arose from mutations in specific S protein domains and subdomains. The results reveal the inter-domain networks controlling S protein dynamics and efficiencies of entry steps, and they offer insights on the evolution of SARS-CoV-2 variants that arise and ultimately dominate infections worldwide.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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42
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Wang G, Liu X, Wang K, Gao Y, Li G, Baptista-Hon DT, Yang XH, Xue K, Tai WH, Jiang Z, Cheng L, Fok M, Lau JYN, Yang S, Lu L, Zhang P, Zhang K. Deep-learning-enabled protein-protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution. Nat Med 2023; 29:2007-2018. [PMID: 37524952 DOI: 10.1038/s41591-023-02483-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023]
Abstract
Host-pathogen interactions and pathogen evolution are underpinned by protein-protein interactions between viral and host proteins. An understanding of how viral variants affect protein-protein binding is important for predicting viral-host interactions, such as the emergence of new pathogenic SARS-CoV-2 variants. Here we propose an artificial intelligence-based framework called UniBind, in which proteins are represented as a graph at the residue and atom levels. UniBind integrates protein three-dimensional structure and binding affinity and is capable of multi-task learning for heterogeneous biological data integration. In systematic tests on benchmark datasets and further experimental validation, UniBind effectively and scalably predicted the effects of SARS-CoV-2 spike protein variants on their binding affinities to the human ACE2 receptor, as well as to SARS-CoV-2 neutralizing monoclonal antibodies. Furthermore, in a cross-species analysis, UniBind could be applied to predict host susceptibility to SARS-CoV-2 variants and to predict future viral variant evolutionary trends. This in silico approach has the potential to serve as an early warning system for problematic emerging SARS-CoV-2 variants, as well as to facilitate research on protein-protein interactions in general.
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Affiliation(s)
- Guangyu Wang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China.
| | - Xiaohong Liu
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- UCL Cancer Institute, University College London, London, UK
| | - Kai Wang
- Department of Big Data and Biomedical Artificial Intelligence, National Biomedical Imaging Center, College of Future Technology, Peking University and Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Yuanxu Gao
- Guangzhou National Laboratory, Guangzhou, China
| | - Gen Li
- Guangzhou National Laboratory, Guangzhou, China
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Daniel T Baptista-Hon
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Xiaohong Helena Yang
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Wa Hou Tai
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Zeyu Jiang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China
| | - Linling Cheng
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Manson Fok
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Johnson Yiu-Nam Lau
- Departments of Biology and Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ligong Lu
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Ping Zhang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China
| | - Kang Zhang
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China.
- Department of Big Data and Biomedical Artificial Intelligence, National Biomedical Imaging Center, College of Future Technology, Peking University and Peking-Tsinghua Center for Life Sciences, Beijing, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China.
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43
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Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JPM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC. RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544432. [PMID: 37503026 PMCID: PMC10370179 DOI: 10.1101/2023.06.09.544432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
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Hastie KM, Yu X, Ana-Sosa-Batiz F, Zyla DS, Harkins SS, Hariharan C, Wasserman H, Zandonatti MA, Miller R, Maule E, Kim K, Valentine KM, Shresta S, Saphire EO. Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence. Cell Rep 2023; 42:112421. [PMID: 37083327 PMCID: PMC10083196 DOI: 10.1016/j.celrep.2023.112421] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly emergent strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), particularly those of the Omicron lineage. Here, we report the identification of a panel of vaccinee-derived antibodies that have broad-spectrum neutralization activity. Structural and biochemical characterization of the three broadest-spectrum antibodies reveal complementary footprints and differing requirements for avidity to overcome variant-associated mutations in their binding footprints. In the K18 mouse model of infection, these three antibodies exhibit protective efficacy against BA.1 and BA.2 infection. This study highlights the resilience and vulnerabilities of SARS-CoV-2 antibodies and provides road maps for further development of broad-spectrum therapeutics.
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Affiliation(s)
- Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
| | - Xiaoying Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Fernanda Ana-Sosa-Batiz
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Dawid S Zyla
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Stephanie S Harkins
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Chitra Hariharan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Hal Wasserman
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Michelle A Zandonatti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenneth Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kristen M Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92038, USA.
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Wang Z, Li D, Chen Y, Sun Y, Jin C, Hu C, Feng Y, Su J, Ren L, Hao Y, Wang S, Zhu M, Liu Y, Qi J, Zhu B, Shao Y. Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents. Front Immunol 2023; 14:1160283. [PMID: 37234155 PMCID: PMC10207940 DOI: 10.3389/fimmu.2023.1160283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
INTRODUCTION The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. METHODS In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. RESULTS AND DISCUSSION We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiling Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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46
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Tu B, Gao Y, An X, Wang H, Huang Y. Localized delivery of nanomedicine and antibodies for combating COVID-19. Acta Pharm Sin B 2023; 13:1828-1846. [PMID: 36168329 PMCID: PMC9502448 DOI: 10.1016/j.apsb.2022.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/01/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a major health burden in the world. So far, many strategies have been investigated to control the spread of COVID-19, including social distancing, disinfection protocols, vaccines, and antiviral treatments. Despite the significant achievement, due to the constantly emerging new variants, COVID-19 is still a great challenge to the global healthcare system. It is an urgent demand for the development of new therapeutics and technologies for containing the wild spread of SARS-CoV-2. Inhaled administration is useful for the treatment of lung and respiratory diseases, and enables the drugs to reach the site of action directly with benefits of decreased dose, improved safety, and enhanced patient compliance. Nanotechnology has been extensively applied in the prevention and treatment of COVID-19. In this review, the inhaled nanomedicines and antibodies, as well as intranasal nanodrugs, for the prevention and treatment of COVID-19 are summarized.
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Affiliation(s)
- Bin Tu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanrong Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinran An
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Huiyuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yongzhuo Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, SIMM, CAS, Zhongshan 528437, China
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Shanghai 201203, China
- Taizhou University, School of Advanced Study, Institute of Natural Medicine and Health Product, Taizhou 318000, China
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Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G. Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants. Nat Commun 2023; 14:2179. [PMID: 37069158 PMCID: PMC10107573 DOI: 10.1038/s41467-023-37926-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, we offer insights into the inactivated vaccine-induced antibody responses after prime-boost vaccination at both the polyclonal and monoclonal levels. We characterized the VDJ sequence of 118 monoclonal antibodies (mAbs) and found that 20 neutralizing mAbs showed varied potency and breadth against a range of variants including XBB.1.5, BQ.1.1, and BN.1. Bispecific antibodies (bsAbs) based on nonoverlapping mAbs exhibited enhanced neutralizing potency and breadth against the most antibody-evasive strains, such as XBB.1.5, BQ.1.1, and BN.1. The passive transfer of mAbs or their bsAb effectively protected female hACE2 transgenic mice from challenge with an infectious Delta or Omicron BA.2 variant. The neutralization mechanisms of these antibodies were determined by structural characterization. Overall, a broad spectrum of potent and distinct neutralizing antibodies can be induced in individuals immunized with the SARS-CoV-2 inactivated vaccine BBIBP-CorV, suggesting the application potential of inactivated vaccines and these antibodies for preventing infection by SARS-CoV-2 circulating variants.
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Grants
- National Key R&D Program of China (2021YFC2300200, 2020YFC1200104, 2018YFA0507202, 2021YFC2302405, 2022YFC2302204), the National Natural Science Foundation of China (32188101, 31825001, 81730063, and 81961160737), the Yunnan Cheng gong expert workstation (202005AF150034), Innovation Team Project of Yunnan Science and Technology Department (202105AE160020), and Tsinghua-Foshan Innovation Special Fund (2022THFS6124).
- National Key R&D Program of China (2022YFC2303403)
- National Key R&D Program of China (2021YFC2300104, 2022YFF1203103), the National Natural Science Foundation of China (32171202), and Vanke Special Fund for Public Health and Health Discipline Development, Tsinghua University (20221080056).
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Affiliation(s)
- Yubin Liu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinyu Zhuang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Zhicheng Chen
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Yan Zou
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Jie Sheng
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Tianpeng Li
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Wanbo Tai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Yunfeng Chen
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Liangqin Tong
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xi Yu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Linjuan Wu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Dong Chen
- Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Renli Zhang
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Weijun Shen
- Center for Translational Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China.
| | - Mingyao Tian
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Gong Cheng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China.
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Montcho Y, Nalwanga R, Azokpota P, Doumatè JT, Lokonon BE, Salako VK, Wolkewitz M, Glèlè Kakaï R. Assessing the Impact of Vaccination on the Dynamics of COVID-19 in Africa: A Mathematical Modeling Study. Vaccines (Basel) 2023; 11:vaccines11040857. [PMID: 37112769 PMCID: PMC10144609 DOI: 10.3390/vaccines11040857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Several effective COVID-19 vaccines are administered to combat the COVID-19 pandemic globally. In most African countries, there is a comparatively limited deployment of vaccination programs. In this work, we develop a mathematical compartmental model to assess the impact of vaccination programs on curtailing the burden of COVID-19 in eight African countries considering SARS-CoV-2 cumulative case data for each country for the third wave of the COVID-19 pandemic. The model stratifies the total population into two subgroups based on individual vaccination status. We use the detection and death rates ratios between vaccinated and unvaccinated individuals to quantify the vaccine's effectiveness in reducing new COVID-19 infections and death, respectively. Additionally, we perform a numerical sensitivity analysis to assess the combined impact of vaccination and reduction in the SARS-CoV-2 transmission due to control measures on the control reproduction number (Rc). Our results reveal that on average, at least 60% of the population in each considered African country should be vaccinated to curtail the pandemic (lower the Rc below one). Moreover, lower values of Rc are possible even when there is a low (10%) or moderate (30%) reduction in the SARS-CoV-2 transmission rate due to NPIs. Combining vaccination programs with various levels of reduction in the transmission rate due to NPI aids in curtailing the pandemic. Additionally, this study shows that vaccination significantly reduces the severity of the disease and death rates despite low efficacy against COVID-19 infections. The African governments need to design vaccination strategies that increase vaccine uptake, such as an incentive-based approach.
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Affiliation(s)
- Yvette Montcho
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
| | - Robinah Nalwanga
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
| | - Paustella Azokpota
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
| | - Jonas Têlé Doumatè
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
- Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Abomey-Calavi, Cotonou 01 BP 526, Benin
| | - Bruno Enagnon Lokonon
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
| | - Valère Kolawole Salako
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
| | - Martin Wolkewitz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg, Germany
| | - Romain Glèlè Kakaï
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou 04 BP 1525, Benin
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Cheng Y, Zheng D, Zhang D, Guo D, Wang Y, Liu W, Liang L, Hu J, Luo T. Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants. J Mol Model 2023; 29:109. [PMID: 36964244 PMCID: PMC10038388 DOI: 10.1007/s00894-023-05509-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023]
Abstract
OBJECTIVE The COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe challenges to people's health and quality of life. A full understanding life cycle of the virus in host cells helps to reveal inactivation mechanism of antibody and provide inspiration for the development of a new-generation vaccines. METHODS In this work, molecular recognitions and conformational changes of SARS-CoV-2 spike protein mutants (i.e., Delta, Mu, and Omicron) and three essential partners (i.e., membrane receptor hACE2, protease TMPRSS2, and antibody C121) both were compared and analyzed using molecular simulations. RESULTS Water basin and binding free energy calculations both show that the three mutants possess higher affinity for hACE2 than WT, exhibiting stronger virus transmission. The descending order of cleavage ability by TMPRSS2 is Mu, Delta, Omicron, and WT, which is related to the new S1/S2 cutting site induced by transposition effect. The inefficient utilization of TMPRSS2 by Omicron is consistent with its primary entry into cells via the endosomal pathway. In addition, RBD-directed antibody C121 showed obvious resistance to Omicron, which may have originated from high fluctuation of approaching angles, high flexibility of I472-F490 loop, and reduced binding ability. CONCLUSIONS According to the overall characteristics of the three mutants, high infectivity, high immune escape, and low virulence may be the future evolutionary selection of SARS-CoV-2. In a word, this work not only proposes the possible resistance mechanism of SARS-CoV-2 mutants, but also provides theoretical guidance for the subsequent drug design against COVID-19 based on S protein structure.
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Affiliation(s)
- Yan Cheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Dan Zheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Derong Zhang
- School of Marxism, Chengdu Vocational & Technical College of Industry, Chengdu, China
| | - Du Guo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China.
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50
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Zhang H, Lv P, Jiang J, Liu Y, Yan R, Shu S, Hu B, Xiao H, Cai K, Yuan S, Li Y. Advances in developing ACE2 derivatives against SARS-CoV-2. THE LANCET. MICROBE 2023; 4:e369-e378. [PMID: 36934742 PMCID: PMC10019897 DOI: 10.1016/s2666-5247(23)00011-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 03/17/2023]
Abstract
Extensive immune evasion of SARS-CoV-2 rendered therapeutic antibodies ineffective in the COVID-19 pandemic. Propagating SARS-CoV-2 variants are characterised by immune evasion capacity through key amino acid mutations, but can still bind human angiotensin-converting enzyme 2 (ACE2) through the spike protein and are, thus, sensitive to ACE2-mimicking decoys as inhibitors. In this Review, we examine advances in the development of ACE2 derivatives from the past 3 years, including the recombinant ACE2 proteins, ACE2-loaded extracellular vesicles, ACE2-mimicking antibodies, and peptide or mini-protein mimetics of ACE2. Several ACE2 derivatives are granted potent neutralisation efficacy against SARS-CoV-2 variants that rival or surpass endogenous antibodies by various auxiliary techniques such as chemical modification and practical recombinant design. The derivatives also represent enhanced production efficiency and improved bioavailability. In addition to these derivatives of ACE2, new effective therapeutics against SARS-CoV-2 variants are expected to be developed.
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Affiliation(s)
- Haoran Zhang
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Panjing Lv
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Jingrui Jiang
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Yahui Liu
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Ruixi Yan
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Sainan Shu
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Han Xiao
- Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Shuai Yuan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Hubei Jiangxia Laboratory, Wuhan, China.
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China; Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.
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