1
|
Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [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: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
Collapse
Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of 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, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| |
Collapse
|
2
|
Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
Collapse
Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
3
|
Tachibana K, Nakamura Y, Do TL, Kihara T, Kawada H, Yamamoto N, Ando K. Mutations in the SARS-CoV-2 spike proteins affected the ACE2-binding affinity during the development of Omicron pandemic variants. Biochem Biophys Res Commun 2024; 719:150120. [PMID: 38759524 DOI: 10.1016/j.bbrc.2024.150120] [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: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Mutations in SARS-CoV-2 caused multiple waves of pandemics. To identify the function of such mutations, we investigated the binding affinity of the S protein with its receptor, ACE2. Omicron BA.1 showed significantly lower binding affinity with human ACE2 than prototype SARS-CoV-2 and Alpha strain, indicating that pre-Omicron to Omicron transition was not mediated by increasing the ACE2-binding affinity. Meanwhile, the later Omicron variants, BA.5 and XBB.1.5, showed significantly higher ACE2-binding affinity, suggesting that the increased ACE2-binding could be involved in the variant transition within Omicron strains. Furthermore, Alpha and Omicron variants, but not prototype SARS-CoV-2, bound mouse ACE2, which lead to a hypothesis that early Omicron strains evolved from Alpha strain by acquiring multiple mutations in mice.
Collapse
Affiliation(s)
- Kouichi Tachibana
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan.
| | - Yoshihiko Nakamura
- Tokai University School of Medicine, Center for Regenerative Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Thi Ly Do
- The University of Kitakyusyu, Department of Life and Environment Engineering, 1-1 Hibikino, Wakamatu, Kitakyusyu, Fukuoka, Japan
| | - Takanori Kihara
- The University of Kitakyusyu, Department of Life and Environment Engineering, 1-1 Hibikino, Wakamatu, Kitakyusyu, Fukuoka, Japan
| | - Hiroshi Kawada
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Norio Yamamoto
- Tokai University School of Medicine, Department of Microbiology, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Kiyoshi Ando
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan
| |
Collapse
|
4
|
Wang Z, Sun W, Li D, Sun Y, Zhu M, Wang W, Zhang Y, Li E, Yan F, Wang T, Feng N, Yang S, Xia X, Gao Y. A live attenuated influenza B virus vaccine expressing RBD elicits protective immunity against SARS-CoV-2 in mice. Virus Res 2024; 345:199378. [PMID: 38643857 PMCID: PMC11059473 DOI: 10.1016/j.virusres.2024.199378] [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: 05/11/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to human health globally. It is crucial to develop a vaccine to reduce the effect of the virus on public health, economy, and society and regulate the transmission of SARS-CoV-2. Influenza B virus (IBV) can be used as a vector that does not rely on the current circulating influenza A strains. In this study, we constructed an IBV-based vector vaccine by inserting a receptor-binding domain (RBD) into a non-structural protein 1 (NS1)-truncated gene (rIBV-NS110-RBD). Subsequently, we assessed its safety, immunogenicity, and protective efficacy against SARS-CoV-2 in mice, and observed that it was safe in a mouse model. Intranasal administration of a recombinant rIBV-NS110-RBD vaccine induced high levels of SARS-CoV-2-specific IgA and IgG antibodies and T cell-mediated immunity in mice. Administering two doses of the intranasal rIBV-NS110-RBD vaccine significantly reduced the viral load and lung damage in mice. This novel IBV-based vaccine offers a novel approach for controlling the SARS-CoV-2 pandemic.
Collapse
MESH Headings
- Animals
- Mice
- Influenza B virus/immunology
- Influenza B virus/genetics
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- COVID-19/prevention & control
- COVID-19/immunology
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/administration & dosage
- Vaccines, Attenuated/genetics
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Mice, Inbred BALB C
- Female
- Administration, Intranasal
- Humans
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Immunoglobulin A/blood
- Disease Models, Animal
- Immunoglobulin G/blood
- Viral Load
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
Collapse
Affiliation(s)
- Zhenfei Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; College of Animal Science and Technology, College of Veterinary and Medicine, Jilin Agricultural University, Changchun, China
| | - Weiyang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Dongxu Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, PR China
| | - Menghan Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Henan International Joint Laboratory for Nuclear Protein Regulation, Henan University, School of Basic Medical Sciences, Kaifeng, China
| | - Wenqi Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yiming Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| |
Collapse
|
5
|
He L, Wu Q, Zhang Z, Chen L, Yu K, Li L, Jia Q, Wang Y, Ni J, Wang C, Li Q, Zhai X, Zhao J, Liu Y, Fan R, Li YP. Development of Broad-Spectrum Nanobodies for the Therapy and Diagnosis of SARS-CoV-2 and Its Multiple Variants. Mol Pharm 2024. [PMID: 38920116 DOI: 10.1021/acs.molpharmaceut.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evaded the efficacy of previously developed antibodies and vaccines, thus remaining a significant global public health threat. Therefore, it is imperative to develop additional antibodies that are capable of neutralizing emerging variants. Nanobodies, as the smallest functional single-domain antibodies, exhibit enhanced stability and penetration ability, enabling them to recognize numerous concealed epitopes that are inaccessible to conventional antibodies. Herein, we constructed an immune library based on the immunization of alpaca with the S1 subunit of the SARS-CoV-2 spike protein, from which two nanobodies, Nb1 and Nb2, were selected using phage display technology for further characterization. Both nanobodies, with the binding residues residing within the receptor-binding domain (RBD) region of the spike, exhibited high affinity toward the S1 subunit. Moreover, they displayed cross-neutralizing activity against both wild-type SARS-CoV-2 and 10 ο variants, including BA.1, BA.2, BA.3, BA.5, BA.2.75, BF.7, BQ.1, EG.5.1, XBB.1.5, and JN.1. Molecular modeling and dynamics simulations predicted that both nanobodies interacted with the viral RBD through their complementarity determining region 1 (CDR1) and CDR2. These two nanobodies are novel tools for the development of therapeutic and diagnostic countermeasures targeting SARS-CoV-2 variants and potentially emerging coronaviruses.
Collapse
Affiliation(s)
- Lei He
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qian Wu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, 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 510120, China
| | - Lingling Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Kuai Yu
- 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 510120, China
| | - Leibin Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qiong Jia
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, 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 510120, China
| | - Jianqiang Ni
- China Animal Disease Control Center, Beijing 102618, China
| | - Chuanbin Wang
- China Animal Disease Control Center, Beijing 102618, China
| | - Qi Li
- China Animal Disease Control Center, Beijing 102618, China
| | - Xinyan Zhai
- China Animal Disease Control Center, Beijing 102618, 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 510120, China
| | - Yuliang Liu
- China Animal Disease Control Center, Beijing 102618, China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yi-Ping Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| |
Collapse
|
6
|
Du W, Debski-Antoniak O, Drabek D, van Haperen R, van Dortmondt M, van der Lee J, Drulyte I, van Kuppeveld FJM, Grosveld F, Hurdiss DL, Bosch BJ. Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun 2024; 15:5330. [PMID: 38909062 PMCID: PMC11193727 DOI: 10.1038/s41467-024-49693-0] [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: 12/08/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
Collapse
Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Oliver Debski-Antoniak
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
7
|
Geanes ES, McLennan R, Pierce SH, Menden HL, Paul O, Sampath V, Bradley T. SARS-CoV-2 envelope protein regulates innate immune tolerance. iScience 2024; 27:109975. [PMID: 38827398 PMCID: PMC11140213 DOI: 10.1016/j.isci.2024.109975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024] Open
Abstract
Severe COVID-19 often leads to secondary infections and sepsis that contribute to long hospital stays and mortality. However, our understanding of the precise immune mechanisms driving severe complications after SARS-CoV-2 infection remains incompletely understood. Here, we provide evidence that the SARS-CoV-2 envelope (E) protein initiates innate immune inflammation, via toll-like receptor 2 signaling, and establishes a sustained state of innate immune tolerance following initial activation. Monocytes in this tolerant state exhibit reduced responsiveness to secondary stimuli, releasing lower levels of cytokines and chemokines. Mice exposed to E protein before secondary lipopolysaccharide challenge show diminished pro-inflammatory cytokine expression in the lung, indicating that E protein drives this tolerant state in vivo. These findings highlight the potential of the SARS-CoV-2 E protein to induce innate immune tolerance, contributing to long-term immune dysfunction that could lead to susceptibility to subsequent infections, and uncovers therapeutic targets aimed at restoring immune function following SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Eric S. Geanes
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Stephen H. Pierce
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Heather L. Menden
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Oishi Paul
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Venkatesh Sampath
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
| |
Collapse
|
8
|
Wang D, Zhang Z, Baudys J, Haynes C, Osman SH, Zhou B, Barr JR, Gumbart JC. Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile. ACS Infect Dis 2024; 10:2032-2046. [PMID: 38728322 PMCID: PMC11184558 DOI: 10.1021/acsinfecdis.4c00015] [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: 01/08/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding in proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics and disulfide bonding of recombinant spike proteins derived from the SARS-CoV-2 Omicron variant (B.1.1.529) in comparison with the D614G spike variant. Furthermore, we conducted microsecond-long molecular dynamics simulations on spike proteins to resolve how the different N-glycans impact spike conformational sampling in the two variants. Our findings reveal that the Omicron spike protein maintains an overall resemblance to the D614G spike variant in terms of site-specific glycan processing and disulfide bond formation. Nonetheless, alterations in glycans were observed at certain N-glycosylation sites. These changes, in synergy with mutations within the Omicron spike protein, result in increased surface accessibility of the macromolecule, including the ectodomain, receptor-binding domain, and N-terminal domain. Additionally, mutagenesis and pull-down assays reveal the role of glycosylation of a specific sequon (N149); furthermore, the correlation of MD simulation and HDX-MS identified several high-dynamic areas of the spike proteins. These insights contribute to our understanding of the interplay between structure and function, thereby advancing effective vaccination and therapeutic strategies.
Collapse
Affiliation(s)
- Dongxia Wang
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Zijian Zhang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 United States
| | - Jakub Baudys
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Christopher Haynes
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Sarah H. Osman
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Bin Zhou
- National
Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - John R. Barr
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 United States
| |
Collapse
|
9
|
Runnstrom MC, Lamothe PA, Faliti CE, Cheedarla N, Moreno A, Suthar MS, Nahata R, Ravindran M, Haddad NS, Morrison-Porter A, Quehl H, Ramonell RP, Woodruff M, Anam F, Zhang R, Swenson C, Polito C, Neveu W, Patel R, Smirnova N, Nguyen DC, Kim C, Hentenaar I, Kyu S, Usman S, Ngo T, Guo Z, Wu H, Daiss JL, Park J, Manning KE, Wali B, Ellis ML, Sharma S, Holguin F, Cheedarla S, Neish AS, Roback JD, Sanz I, Eun-Hyung Lee F. Patients taking benralizumab, dupilumab, or mepolizumab have lower postvaccination SARS-CoV-2 immunity. J Allergy Clin Immunol 2024:S0091-6749(24)00420-2. [PMID: 38878020 DOI: 10.1016/j.jaci.2024.03.029] [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: 09/22/2023] [Revised: 02/27/2024] [Accepted: 03/15/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Biologic therapies inhibiting the IL-4 or IL-5 pathways are very effective in the treatment of asthma and other related conditions. However, the cytokines IL-4 and IL-5 also play a role in the generation of adaptive immune responses. Although these biologics do not cause overt immunosuppression, their effect in primary severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunization has not been studied completely. OBJECTIVE Our aim was to evaluate the antibody and cellular immunity after SARS-CoV-2 mRNA vaccination in patients on biologics (PoBs). METHODS Patients with severe asthma or atopic dermatitis who were taking benralizumab, dupilumab, or mepolizumab and had received the initial dose of the 2-dose adult SARS-CoV-2 mRNA vaccine were enrolled in a prospective, observational study. As our control group, we used a cohort of immunologically healthy subjects (with no significant immunosuppression) who were not taking biologics (NBs). We used a multiplexed immunoassay to measure antibody levels, neutralization assays to assess antibody function, and flow cytometry to quantitate Spike-specific lymphocytes. RESULTS We analyzed blood from 57 patients in the PoB group and 46 control subjects from the NB group. The patients in the PoB group had lower levels of SARS-CoV-2 antibodies, pseudovirus neutralization, live virus neutralization, and frequencies of Spike-specific B and CD8 T cells at 6 months after vaccination. In subgroup analyses, patients with asthma who were taking biologics had significantly lower pseudovirus neutralization than did subjects with asthma who were not taking biologics. CONCLUSION The patients in the PoB group had reduced SARS-CoV-2-specific antibody titers, neutralizing activity, and virus-specific B- and CD8 T-cell counts. These results have implications when considering development of a more individualized immunization strategy in patients who receive biologic medications blocking IL-4 or IL-5 pathways.
Collapse
Affiliation(s)
- Martin C Runnstrom
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Department of Medicine, Atlanta Veterans Affairs Healthcare System, Atlanta, Ga
| | - Pedro A Lamothe
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Caterina E Faliti
- Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Lowance Center for Human Immunology, Atlanta, Ga
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Alberto Moreno
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Yerkes National Primate Research Center, Atlanta, Ga
| | - Mehul S Suthar
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Ga; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Rishika Nahata
- Emory College of Arts and Sciences, Emory University, Atlanta, Ga
| | - Mayuran Ravindran
- J. Willis Hurst Internal Medicine Residency Program, Emory University School of Medicine, Atlanta, Ga
| | - Natalie S Haddad
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Andrea Morrison-Porter
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Hannah Quehl
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Richard P Ramonell
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Matthew Woodruff
- Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Lowance Center for Human Immunology, Atlanta, Ga
| | - Fabliha Anam
- Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Lowance Center for Human Immunology, Atlanta, Ga
| | - Rebeca Zhang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Ga
| | - Colin Swenson
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Carmen Polito
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Wendy Neveu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Rahulkumar Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Natalia Smirnova
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Doan C Nguyen
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Lowance Center for Human Immunology, Atlanta, Ga
| | - Caroline Kim
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Ian Hentenaar
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Shuya Kyu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Sabeena Usman
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Thuy Ngo
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Zhenxing Guo
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Ga
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Ga
| | - John L Daiss
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Jiwon Park
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Kelly E Manning
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Ga; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Bursha Wali
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Ga; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Madison L Ellis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Ga; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Colo
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Colo
| | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Ga
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Ga
| | - Ignacio Sanz
- Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, Ga; Lowance Center for Human Immunology, Atlanta, Ga
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Ga.
| |
Collapse
|
10
|
Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 2024; 13:RP95708. [PMID: 38864493 PMCID: PMC11168744 DOI: 10.7554/elife.95708] [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] [Indexed: 06/13/2024] Open
Abstract
Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N-glycosylation at N343 and how this glycan's structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
Collapse
Affiliation(s)
- Callum M Ives
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | - Linh Nguyen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Carl A Fogarty
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | | | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council CanadaQuébecCanada
- Département de Biochimie et Médecine Moléculaire, Université de MontréalQuébecCanada
| | - John Klassen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Elisa Fadda
- School of Biological Sciences, University of SouthamptonSouthamptonUnited Kingdom
| |
Collapse
|
11
|
Bruun TU, Do J, Weidenbacher PAB, Kim PS. Engineering a SARS-CoV-2 vaccine targeting the RBD cryptic-face via immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597541. [PMID: 38895327 PMCID: PMC11185595 DOI: 10.1101/2024.06.05.597541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the main target of neutralizing antibodies. Although they are infrequently elicited during infection or vaccination, antibodies that bind to the conformation-specific cryptic face of the RBD display remarkable breadth of binding and neutralization across Sarbecoviruses. Here, we employed the immunofocusing technique PMD (protect, modify, deprotect) to create RBD immunogens (PMD-RBD) specifically designed to focus the antibody response towards the cryptic-face epitope recognized by the broadly neutralizing antibody S2X259. Immunization with PMD-RBD antigens induced robust binding titers and broad neutralizing activity against homologous and heterologous Sarbecovirus strains. A serum-depletion assay provided direct evidence that PMD successfully skewed the polyclonal antibody response towards the cryptic face of the RBD. Our work demonstrates the ability of PMD to overcome immunodominance and refocus humoral immunity, with implications for the development of broader and more resilient vaccines against current and emerging viruses with pandemic potential.
Collapse
Affiliation(s)
- Theodora U.J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
| | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
| | - Payton A.-B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| |
Collapse
|
12
|
Lin S, Wang X, Tang RWL, Duan R, Leung KW, Dong TTX, Webb SE, Miller AL, Tsim KWK. Computational Docking as a Tool in Guiding the Drug Design of Rutaecarpine Derivatives as Potential SARS-CoV-2 Inhibitors. Molecules 2024; 29:2636. [PMID: 38893512 PMCID: PMC11173897 DOI: 10.3390/molecules29112636] [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: 05/17/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
COVID-19 continues to spread around the world. This is mainly because new variants of the SARS-CoV-2 virus emerge due to genomic mutations, evade the immune system and result in the effectiveness of current therapeutics being reduced. We previously established a series of detection platforms, comprising computational docking analysis, S-protein-based ELISA, pseudovirus entry, and 3CL protease activity assays, which allow us to screen a large library of phytochemicals from natural products and to determine their potential in blocking the entry of SARS-CoV-2. In this new screen, rutaecarpine (an alkaloid from Evodia rutaecarpa) was identified as exhibiting anti-SARS-CoV-2 activity. Therefore, we conducted multiple rounds of structure-activity-relationship (SAR) studies around this phytochemical and generated several rutaecarpine analogs that were subjected to in vitro evaluations. Among these derivatives, RU-75 and RU-184 displayed remarkable inhibitory activity when tested in the 3CL protease assay, S-protein-based ELISA, and pseudovirus entry assay (for both wild-type and omicron variants), and they attenuated the inflammatory response induced by SARS-CoV-2. Interestingly, RU-75 and RU-184 both appeared to be more potent than rutaecarpine itself, and this suggests that they might be considered as lead candidates for future pharmacological elaboration.
Collapse
Affiliation(s)
- Shengying Lin
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiaoyang Wang
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Roy Wai-Lun Tang
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ran Duan
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ka Wing Leung
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tina Ting-Xia Dong
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Sarah E. Webb
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Andrew L. Miller
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Karl Wah-Keung Tsim
- Center for Chinese Medicine, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (R.D.); (K.W.L.); (T.T.-X.D.); (S.E.W.); (A.L.M.)
- State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| |
Collapse
|
13
|
Cui L, Li T, Xue W, Zhang S, Wang H, Liu H, Gu Y, Xia N, Li S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024; 16:900. [PMID: 38932192 DOI: 10.3390/v16060900] [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: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about the possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories of broadly neutralizing antibodies (bnAbs) that retain prominent effectiveness against emerging variants including Omicron sub-lineages. The molecular characteristics, epitope conservation, and resistance mechanisms of these antibodies are further detailed, aiming to offer suggestion or direction for the development of therapeutic antibodies, and facilitate the design of vaccines with broad-spectrum potential.
Collapse
Affiliation(s)
- Lingyan Cui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Wenhui Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hong Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hongjing Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| |
Collapse
|
14
|
Biswas D, Mahalingam G, Subaschandrabose RK, Priya S, Ramachandran R, Suresh S, Mathivanan TV, Balu NV, Selvaraj K, Nellickal AJ, Christudoss P, Samuel P, Kt RD, Marepally S, Moorthy M. Role of prior immunity in binding to spike of "future" Omicron subvariants. Indian J Med Microbiol 2024; 50:100615. [PMID: 38782260 DOI: 10.1016/j.ijmmb.2024.100615] [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: 11/11/2023] [Revised: 04/18/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Throughout the COVID-19 pandemic, virus evolution and large-scale vaccination programs have caused multiple exposures to SARS CoV-2 spike protein, resulting in complex antibody profiles. The binding of these to spike protein of "future" variants in the context of such heterogeneous exposure has not been studied. METHODS We tested archival sera (Delta and Omicron period) stratified by anti-spike antibody (including IgG) levels for reactivity to Omicron-subvariants(BA.1, BA.2,BA.2.12.1, BA.2.75, BA.4/5 and BF.7) spike protein. Assessed antigenic distance between groups using Antigenic Cartography and performed hierarchical clustering of antibody data in a Euclidean distance framework. RESULTS Antibody (including IgG) antibody reactivity to Wild-type (CLIA) and subvariants (ELISA) spike protein were similar between periods (p > 0.05). Both 'High S' and 'Low S' of Delta and Omicron periods were closely related to "future" subvariants by Antigenic Cartography. Sera from different S groups clustered together with 'Low S' interspersed between 'High S' on hierarchical clustering, suggesting common binding sites. Further, anti-spike antibodies (including IgG) to Wild-type (S1/S2 and Trimeric S) clustered with Omicron-subvariant binding antibodies. CONCLUSIONS Hybrid immunity caused by cumulative virus exposure in Delta or Omicron periods resulted in equivalent binding to "future" variants, which might be due to binding to conserved regions of spike protein of future variants. A prominent finding is that the 'Low S' antibody demonstrates similar binding.
Collapse
Affiliation(s)
- Deepayan Biswas
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | | | - Sangeetha Priya
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Rohini Ramachandran
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Sevanthy Suresh
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Tamil Venthan Mathivanan
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Nelson Vijaykumar Balu
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Kavitha Selvaraj
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Arun Jose Nellickal
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Pamela Christudoss
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Prasanna Samuel
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, Pin: 632002, India.
| | - Ramya Devi Kt
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram, Tamil Nadu, Pin: 603203, India.
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| |
Collapse
|
15
|
Sun B, Chen Z, Feng B, Chen S, Feng S, Wang Q, Niu X, Zhang Z, Zheng P, Lin M, Luo J, Pan Y, Guan S, Zhong N, Chen L. Development of a colloidal gold-based immunochromatographic assay for rapid detection of nasal mucosal secretory IgA against SARS-CoV-2. Front Microbiol 2024; 15:1386891. [PMID: 38881666 PMCID: PMC11177785 DOI: 10.3389/fmicb.2024.1386891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction Infection with SARS-CoV-2 begins in the upper respiratory tract and can trigger the production of mucosal spike-specific secretory IgA (sIgA), which provides protection against reinfection. It has been recognized that individuals with high level of nasal spike-specific IgA have a lower risk of reinfection. However, mucosal spike-specific sIgA wanes over time, and different individuals may have various level of spike-specific sIgA and descending kinetics, leading to individual differences in susceptibility to reinfection. A method for detecting spike-specific sIgA in the nasal passage would be valuable for predicting the risk of reinfection so that people at risk can have better preparedness. Methods In this study, we describe the development of a colloidal gold-based immunochromatographic (ICT) strip for detecting SARS-CoV-2 Omicron spike-specific sIgA in nasal mucosal lining fluids (NMLFs). Results The ICT strip was designed to detect 0.125 μg or more spike-specific sIgA in 80 μL of NMLFs collected using a nasal swab. Purified nasal sIgA samples from individuals who recently recovered from an Omicron BA.5 infection were used to demonstrate that this ICT strip can specifically detect spike-specific sIgA. The signal levels positively correlated with neutralizing activities against XBB. Subsequent analysis revealed that people with low or undetectable levels of spike-specific sIgA in the nasal passage were more susceptible to SARS-CoV-2 reinfection. Conclusions This nasal spike-specific sIgA ICT strip provides a non-invasive, rapid, and convenient method to assess the risk of reinfection for achieving precision preparedness.
Collapse
Affiliation(s)
- Baoqing Sun
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Zhilong Chen
- Xiamen United Institute of Respiratory Health, Xiamen, China
- Xiamen Fortune Bio. Co., Ltd, Xiamen, China
| | - Bo Feng
- Guangzhou Laboratory, Guangzhou, China
| | - Si Chen
- Guangzhou Laboratory, Guangzhou, China
| | | | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhengyuan Zhang
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Peiyan Zheng
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ming Lin
- Xiamen United Institute of Respiratory Health, Xiamen, China
- Xiamen Fortune Bio. Co., Ltd, Xiamen, China
| | - Jia Luo
- Xiamen United Institute of Respiratory Health, Xiamen, China
- Xiamen Fortune Bio. Co., Ltd, Xiamen, China
| | - Yingxian Pan
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
16
|
Liu C, Xu S, Zheng Y, Xie Y, Xu K, Chai Y, Luo T, Dai L, Gao GF. Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses. Cell Rep 2024; 43:114235. [PMID: 38748880 DOI: 10.1016/j.celrep.2024.114235] [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: 09/06/2023] [Revised: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Nanoparticle vaccines displaying mosaic receptor-binding domains (RBDs) or spike (S) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or other sarbecoviruses are used in preparedness against potential zoonotic outbreaks. Here, we describe a self-assembling nanoparticle using lumazine synthase (LuS) as the scaffold to display RBDs from different sarbecoviruses. Mosaic nanoparticles induce sarbecovirus cross-neutralizing antibodies comparable to a nanoparticle cocktail. We find mosaic nanoparticles elicit a B cell receptor repertoire using an immunodominant germline gene pair of IGHV14-3:IGKV14-111. Most of the tested IGHV14-3:IGKV14-111 monoclonal antibodies (mAbs) are broadly cross-reactive to clade 1a, 1b, and 3 sarbecoviruses. Using mAb competition and cryo-electron microscopy, we determine that a representative IGHV14-3:IGKV14-111 mAb, M2-7, binds to a conserved epitope on the RBD, largely overlapping with the pan-sarbecovirus mAb S2H97. This suggests mosaic nanoparticles expand B cell recognition of the common epitopes shared by different clades of sarbecoviruses. These results provide immunological insights into the cross-reactive responses elicited by mosaic nanoparticles against sarbecoviruses.
Collapse
Affiliation(s)
- Chuanyu Liu
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Senyu Xu
- Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxuan Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingrong Luo
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
17
|
Cohen AA, Keeffe JR, Schiepers A, Dross SE, Greaney AJ, Rorick AV, Gao H, Gnanapragasam PNP, Fan C, West AP, Ramsingh AI, Erasmus JH, Pata JD, Muramatsu H, Pardi N, Lin PJC, Baxter S, Cruz R, Quintanar-Audelo M, Robb E, Serrano-Amatriain C, Magneschi L, Fotheringham IG, Fuller DH, Victora GD, Bjorkman PJ. Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.576722. [PMID: 38370696 PMCID: PMC10871317 DOI: 10.1101/2024.02.08.576722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.
Collapse
Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Sandra E Dross
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Allison J Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Janice D Pata
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott Baxter
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Rita Cruz
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Martina Quintanar-Audelo
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
- Present address: Centre for Inflammation Research and Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Ellis Robb
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | | | - Leonardo Magneschi
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Ian G Fotheringham
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
| |
Collapse
|
18
|
Ramos-Duarte VA, Orlowski A, Jaquenod de Giusti C, Corigliano MG, Legarralde A, Mendoza-Morales LF, Atela A, Sánchez MA, Sander VA, Angel SO, Clemente M. Safe plant Hsp90 adjuvants elicit an effective immune response against SARS-CoV2-derived RBD antigen. Vaccine 2024; 42:3355-3364. [PMID: 38631949 DOI: 10.1016/j.vaccine.2024.04.036] [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: 01/08/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
To better understand the role of pHsp90 adjuvant in immune response modulation, we proposed the use of the Receptor Binding Domain (RBD) of the Spike protein of SARS-CoV2, the principal candidate in the design of subunit vaccines. We evaluated the humoral and cellular immune responses against RBD through the strategy "protein mixture" (Adjuvant + Antigen). The rRBD adjuvanted with rAtHsp81.2 group showed a higher increase of the anti-rRBD IgG1, while the rRBD adjuvanted with rNbHsp90.3 group showed a significant increase in anti-rRBD IgG2b/2a. These results were consistent with the cellular immune response analysis. Spleen cell cultures from rRBD + rNbHsp90.3-immunized mice showed significantly increased IFN-γ production. In contrast, spleen cell cultures from rRBD + rAtHsp81.2-immunized mice showed significantly increased IL-4 levels. Finally, vaccines adjuvanted with rNbHsp90.3 induced higher neutralizing antibody responses compared to those adjuvanted with rAtHsp81.2. To know whether both chaperones must form complexes to generate an effective immune response, we performed co-immunoprecipitation (co-IP) assays. The results indicated that the greater neutralizing capacity observed in the rRBD adjuvanted with rNbHsp90.3 group would be given by the rRBD-rNbHsp90.3 interaction rather than by the quality of the immune response triggered by the adjuvants. These results, together with our previous results, provide a comparative benchmark of these two novel and safe vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV2 subunit vaccines. Furthermore, these results revealed differences in the ability to modulate the immune response between these two pHsp90s, highlighting the importance of adjuvant selection for future rational vaccine and adjuvant design.
Collapse
MESH Headings
- Animals
- Female
- Humans
- Mice
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Vaccine
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- COVID-19/prevention & control
- COVID-19/immunology
- COVID-19 Vaccines/immunology
- HSP90 Heat-Shock Proteins/immunology
- Immunity, Cellular
- Immunity, Humoral
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Mice, Inbred BALB C
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/administration & dosage
Collapse
Affiliation(s)
- Victor A Ramos-Duarte
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Alejandro Orlowski
- Centro de Investigaciones Cardiovasculares "Dr. Horacio E. Cingolani" (CONICET), Universidad Nacional de La Plata, Facultad de Ciencias Médicas, La Plata, Argentina
| | - Carolina Jaquenod de Giusti
- Centro de Investigaciones Cardiovasculares "Dr. Horacio E. Cingolani" (CONICET), Universidad Nacional de La Plata, Facultad de Ciencias Médicas, La Plata, Argentina
| | - Mariana G Corigliano
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Ariel Legarralde
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Luisa F Mendoza-Morales
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Biotecnologías en Bovinos y Ovinos, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Provincia de Buenos Aires, Argentina
| | - Agustín Atela
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Manuel A Sánchez
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Valeria A Sander
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Biotecnologías en Bovinos y Ovinos, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Provincia de Buenos Aires, Argentina
| | - Sergio O Angel
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Parasitología Molecular-UB2, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires, Argentina
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina.
| |
Collapse
|
19
|
Li J, Huang Q, Liang Y, Jiang J, Yang Y, Feng J, Tan X, Li T. The Potential Mechanisms of Arrhythmia in Coronavirus disease-2019. Int J Med Sci 2024; 21:1366-1377. [PMID: 38818469 PMCID: PMC11134579 DOI: 10.7150/ijms.94578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) leads to coronavirus disease-2019 (COVID-19) which can cause severe cardiovascular complications including myocardial injury, arrhythmias, acute coronary syndrome and others. Among these complications, arrhythmias are considered serious and life-threatening. Although arrhythmias have been associated with factors such as direct virus invasion leading to myocardial injury, myocarditis, immune response disorder, cytokine storms, myocardial ischemia/hypoxia, electrolyte abnormalities, intravascular volume imbalances, drug interactions, side effects of COVID-19 vaccines and autonomic nervous system dysfunction, the exact mechanisms of arrhythmic complications in patients with COVID-19 are complex and not well understood. In the present review, the literature was extensively searched to investigate the potential mechanisms of arrhythmias in patients with COVID-19. The aim of the current review is to provide clinicians with a comprehensive foundation for the prevention and treatment of arrhythmias associated with long COVID-19.
Collapse
Affiliation(s)
- Jianhong Li
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Qiuyuan Huang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Yifan Liang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Jun Jiang
- Department of General Surgery (Thyroid Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Yan Yang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Jian Feng
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Tao Li
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| |
Collapse
|
20
|
Mizuno Y, Nakasone W, Nakamura M, Otaki JM. In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development. Vaccines (Basel) 2024; 12:539. [PMID: 38793790 PMCID: PMC11125730 DOI: 10.3390/vaccines12050539] [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: 04/30/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Spike protein sequences in SARS-CoV-2 have been employed for vaccine epitopes, but many short constituent sequences (SCSs) in the spike protein are present in the human proteome, suggesting that some anti-spike antibodies induced by infection or vaccination may be autoantibodies against human proteins. To evaluate this possibility of "molecular mimicry" in silico and in vitro, we exhaustively identified common SCSs (cSCSs) found both in spike and human proteins bioinformatically. The commonality of SCSs between the two systems seemed to be coincidental, and only some cSCSs were likely to be relevant to potential self-epitopes based on three-dimensional information. Among three antibodies raised against cSCS-containing spike peptides, only the antibody against EPLDVL showed high affinity for the spike protein and reacted with an EPLDVL-containing peptide from the human unc-80 homolog protein. Western blot analysis revealed that this antibody also reacted with several human proteins expressed mainly in the small intestine, ovary, and stomach. Taken together, these results showed that most cSCSs are likely incapable of inducing autoantibodies but that at least EPLDVL functions as a self-epitope, suggesting a serious possibility of infection-induced or vaccine-induced autoantibodies in humans. High-risk cSCSs, including EPLDVL, should be excluded from vaccine epitopes to prevent potential autoimmune disorders.
Collapse
Affiliation(s)
- Yuya Mizuno
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Wataru Nakasone
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Morikazu Nakamura
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| |
Collapse
|
21
|
Cornejo A, Franco C, Rodriguez-Nuñez M, García A, Belisario I, Mayora S, Garzaro DJ, Zambrano JL, Jaspe RC, Hidalgo M, Parra-Giménez N, Claro FE, Liprandi F, de Waard JH, Rangel HR, Pujol FH. Humoral Immunity across the SARS-CoV-2 Spike after Sputnik V (Gam-COVID-Vac) Vaccination. Antibodies (Basel) 2024; 13:41. [PMID: 38804309 PMCID: PMC11130906 DOI: 10.3390/antib13020041] [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: 03/20/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
SARS-CoV-2 vaccines have contributed to attenuating the burden of the COVID-19 pandemic by promoting the development of effective immune responses, thus reducing the spread and severity of the pandemic. A clinical trial with the Sputnik-V vaccine was conducted in Venezuela from December 2020 to July 2021. The aim of this study was to explore the antibody reactivity of vaccinated individuals towards different regions of the spike protein (S). Neutralizing antibody (NAb) activity was assessed using a commercial surrogate assay, detecting NAbs against the receptor-binding domain (RBD), and a plaque reduction neutralization test. NAb levels were correlated with the reactivity of the antibodies to the spike regions over time. The presence of Abs against nucleoprotein was also determined to rule out the effect of exposure to the virus during the clinical trial in the serological response. A high serological reactivity was observed to S and specifically to S1 and the RBD. S2, although recognized with lower intensity by vaccinated individuals, was the subunit exhibiting the highest cross-reactivity in prepandemic sera. This study is in agreement with the high efficacy reported for the Sputnik V vaccine and shows that this vaccine is able to induce an immunity lasting for at least 180 days. The dissection of the Ab reactivity to different regions of S allowed us to identify the relevance of epitopes outside the RBD that are able to induce NAbs. This research may contribute to the understanding of vaccine immunity against SARS-CoV-2, which could contribute to the design of future vaccine strategies.
Collapse
Affiliation(s)
- Alejandro Cornejo
- Laboratorio de Bioquímica Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela;
| | - Christopher Franco
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Mariajose Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Alexis García
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Inirida Belisario
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Soriuska Mayora
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Domingo José Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Nereida Parra-Giménez
- Laboratorio de Fisiología de Parásitos, Centro Biofísica y Bioquímica, IVIC, Caracas 1020A, Venezuela;
| | - Franklin Ennodio Claro
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Jacobus Henri de Waard
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| |
Collapse
|
22
|
Kumawat P, Agarwal LK, Sharma K. An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies. Curr Microbiol 2024; 81:169. [PMID: 38733424 DOI: 10.1007/s00284-024-03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/18/2024] [Indexed: 05/13/2024]
Abstract
The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.
Collapse
Affiliation(s)
- Pooja Kumawat
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| |
Collapse
|
23
|
Yuan M, Wilson IA. The D Gene in CDR H3 Determines a Public Class of Human Antibodies to SARS-CoV-2. Vaccines (Basel) 2024; 12:467. [PMID: 38793718 PMCID: PMC11126049 DOI: 10.3390/vaccines12050467] [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: 03/30/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Public antibody responses have been found against many infectious agents. Structural convergence of public antibodies is usually determined by immunoglobulin V genes. Recently, a human antibody public class against SARS-CoV-2 was reported, where the D gene (IGHD3-22) encodes a common YYDxxG motif in heavy-chain complementarity-determining region 3 (CDR H3), which determines specificity for the receptor-binding domain (RBD). In this review, we discuss the isolation, structural characterization, and genetic analyses of this class of antibodies, which have been isolated from various cohorts of COVID-19 convalescents and vaccinees. All eleven YYDxxG antibodies with available structures target the SARS-CoV-2 RBD in a similar binding mode, where the CDR H3 dominates the interaction with antigen. The antibodies target a conserved site on the RBD that does not overlap with the receptor-binding site, but their particular angle of approach results in direct steric hindrance to receptor binding, which enables both neutralization potency and breadth. We also review the properties of CDR H3-dominant antibodies that target other human viruses. Overall, unlike most public antibodies, which are identified by their V gene usage, this newly discovered public class of YYDxxG antibodies is dominated by a D-gene-encoded motif and uncovers further opportunities for germline-targeting vaccine design.
Collapse
Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
24
|
Jackson S, Marshall JL, Mawer A, Lopez-Ramon R, Harris SA, Satti I, Hughes E, Preston-Jones H, Cabrera Puig I, Longet S, Tipton T, Laidlaw S, Doherty RP, Morrison H, Mitchell R, Tanner R, Ateere A, Stylianou E, Wu MS, Fredsgaard-Jones TPW, Breuer J, Rapeport G, Ferreira VM, Gleeson F, Pollard AJ, Carroll M, Catchpole A, Chiu C, McShane H. Safety, tolerability, viral kinetics, and immune correlates of protection in healthy, seropositive UK adults inoculated with SARS-CoV-2: a single-centre, open-label, phase 1 controlled human infection study. THE LANCET. MICROBE 2024:S2666-5247(24)00025-9. [PMID: 38703782 DOI: 10.1016/s2666-5247(24)00025-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND A SARS-CoV-2 controlled human infection model (CHIM) has been successfully established in seronegative individuals using a dose of 1×101 50% tissue culture infectious dose (TCID50) pre-alpha SARS-CoV-2 virus. Given the increasing prevalence of seropositivity to SARS-CoV-2, a CHIM that could be used for vaccine development will need to induce infection in those with pre-existing immunity. Our aim was to find a dose of pre-alpha SARS-CoV-2 virus that induced infection in previously infected individuals. METHODS Healthy, UK volunteers aged 18-30 years, with proven (quantitative RT-PCR or lateral flow antigen test) previous SARS-CoV-2 infection (with or without vaccination) were inoculated intranasally in a stepwise dose escalation CHIM with either 1×101, 1×102, 1×10³, 1×104, or 1×105 TCID50 SARS-CoV-2/human/GBR/484861/2020, the same virus used in the seronegative CHIM. Post-inoculation, volunteers were quarantined in functionally negative pressure rooms (Oxford, UK) for 14 days and until 12-hourly combined oropharyngeal-nasal swabs were negative for viable virus by focus-forming assay. Outpatient follow-up continued for 12 months post-enrolment, with additional visits for those who developed community-acquired SARS-CoV-2 infection. The primary objective was to identify a safe, well tolerated dose that induced infection (defined as two consecutive SARS-CoV-2 positive PCRs starting 24 h after inoculation) in 50% of seropositive volunteers. This study is registered with ClinicalTrials.gov (NCT04864548); enrolment and follow-up to 12 months post-enrolment are complete. FINDINGS Recruitment commenced on May 6, 2021, with the last volunteer enrolled into the dose escalation cohort on Nov 24, 2022. 36 volunteers were enrolled, with four to eight volunteers inoculated in each dosing group from 1×101 to 1×105 TCID50 SARS-CoV-2. All volunteers have completed quarantine, with follow-up to 12 months complete. Despite dose escalation to 1×105 TCID50, we were unable to induce sustained infection in any volunteers. Five (14%) of 36 volunteers were considered to have transient infection, based on the kinetic of their PCR-positive swabs. Transiently infected volunteers had significantly lower baseline mucosal and systemic SARS-CoV-2-specific antibody titres and significantly lower peripheral IFNγ responses against a CD8+ T-cell SARS-CoV-2 peptide pool than uninfected volunteers. 14 (39%) of 36 volunteers subsequently developed breakthrough infection with the omicron variant after discharge from quarantine. Most adverse events reported by volunteers in quarantine were mild, with fatigue (16 [44%]) and stuffy nose (16 [44%]) being the most common. There were no serious adverse events. INTERPRETATION Our study demonstrates potent protective immunity induced by homologous vaccination and homologous or heterologous previous SARS-CoV-2 infection. The community breakthrough infections seen with the omicron variant supports the use of newer variants to establish a model with sufficient rate of infection for use in vaccine and therapeutic development. FUNDING Wellcome Trust and Department for Health and Social Care.
Collapse
Affiliation(s)
- Susan Jackson
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Julia L Marshall
- Department of Paediatrics, University of Oxford, Oxford, UK; The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Mawer
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Iman Satti
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Eileen Hughes
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Stephanie Longet
- The Wellcome Centre for Human Genetics and Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Tipton
- The Wellcome Centre for Human Genetics and Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Laidlaw
- The Wellcome Centre for Human Genetics and Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hazel Morrison
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Rachel Tanner
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Alberta Ateere
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Meng-San Wu
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Judith Breuer
- Institute of Child Health, University College London, London, UK
| | - Garth Rapeport
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Fergus Gleeson
- Oxford Radiology Research Unit, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Miles Carroll
- The Wellcome Centre for Human Genetics and Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Helen McShane
- Department of Paediatrics, University of Oxford, Oxford, UK.
| |
Collapse
|
25
|
Behera LM, Gupta PK, Ghosh M, Shadangi S, Rana S. A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2. J Phys Chem B 2024. [PMID: 38657271 DOI: 10.1021/acs.jpcb.4c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus, is the causative agent responsible for the spread of the COVID19 pandemic across the globe. The global impact of the COVID19 pandemic, the successful approval of vaccines for controlling the pandemic, and the further resurgence of COVID19 necessitate the exploration and validation of alternative therapeutic avenues targeting SARS-CoV-2. The initial entry and further invasion by SARS-CoV-2 require strong protein-protein interactions (PPIs) between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptors expressed on the cell surfaces of various tissues. In principle, disruption of the PPIs between the RBD of SARS-CoV-2 and the ACE2 receptor by designer peptides with optimized pharmacology appears to be an ideal choice for potentially preventing viral entry with minimal immunogenicity. In this context, the current study describes a short, synthetic designer peptide (codenamed SR16, ≤18 aa, molecular weight ≤2.5 kDa), which has a few noncoded amino acids, demonstrates a helical conformation in solution, and also engages the RBD of SARS-CoV-2 through a high-affinity interaction, as judged from a battery of biophysical studies. Further, the designer peptide demonstrates resistance to trypsin degradation, appears to be nontoxic to mammalian cells, and also does not induce hemolysis in freshly isolated human erythrocytes. In summary, SR16 appears to be an ideal peptide binder targeting the RBD of SARS-CoV-2, which has the potential for further optimization and development as an antiviral agent targeting SARS-CoV-2.
Collapse
Affiliation(s)
- Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Sucharita Shadangi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| |
Collapse
|
26
|
Park S, Choi J, Lee Y, Noh J, Kim N, Lee J, Cho G, Kim S, Yoo DK, Kang CK, Choe PG, Kim NJ, Park WB, Kim S, Oh MD, Kwon S, Chung J. An ancestral SARS-CoV-2 vaccine induces anti-Omicron variants antibodies by hypermutation. Nat Commun 2024; 15:3368. [PMID: 38643233 PMCID: PMC11032360 DOI: 10.1038/s41467-024-47743-1] [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: 10/06/2023] [Accepted: 04/10/2024] [Indexed: 04/22/2024] Open
Abstract
The immune escape of Omicron variants significantly subsides by the third dose of an mRNA vaccine. However, it is unclear how Omicron variant-neutralizing antibodies develop under repeated vaccination. We analyze blood samples from 41 BNT162b2 vaccinees following the course of three injections and analyze their B-cell receptor (BCR) repertoires at six time points in total. The concomitant reactivity to both ancestral and Omicron receptor-binding domain (RBD) is achieved by a limited number of BCR clonotypes depending on the accumulation of somatic hypermutation (SHM) after the third dose. Our findings suggest that SHM accumulation in the BCR space to broaden its specificity for unseen antigens is a counterprotective mechanism against virus variant immune escape.
Collapse
Affiliation(s)
- Seoryeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Interdisciplinary Program in Cancer Biology Major, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaewon Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Integrated Major in Innovative Medical Science, Seoul National University, Seoul, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - JinAh Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Geummi Cho
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sujeong Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea.
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Sunghoon Kwon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Interdisciplinary Program in Cancer Biology Major, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
27
|
Garg P, Hsueh SCC, Plotkin SS. Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein. Biophys J 2024; 123:992-1005. [PMID: 38491772 PMCID: PMC11052916 DOI: 10.1016/j.bpj.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/02/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of a conserved S2 epitope located in the central helices below the receptor binding domains would require large-scale motion beyond receptor binding domain up-down motion, but, along the reaction coordinates we explored, it is unlikely to be exposed by such large-scale dynamic fluctuations of the S1 domain without any external facilitating factors, despite some previous computational evidence suggesting transient exposure of this region. Furthermore, glycans, particularly those on N165 and N234, hinder S2-exposing opening dynamics, and thus stabilize spike in addition to immunologically shielding the protein surface. Although the S2 epitope region examined here is central to large-scale conformational changes during viral entry, free energy landscape analysis obtained using the path coordinate formalism reveals no inherent "loaded spring" effect, suggesting that a vaccine immunogen would tend to present the epitope in a prefusion-like conformation and may be effective in neutralization. These findings contribute to a deeper understanding of the dynamic origins of the function of the spike protein, as well as further characterizing the feasibility of the S2 epitope as a therapeutic target.
Collapse
Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
28
|
Salamango DJ. Finally neutralizing the threat? A novel SARS-CoV-2 vaccine platform that elicits enhanced neutralizing antibody responses. mBio 2024; 15:e0006724. [PMID: 38407097 PMCID: PMC11005347 DOI: 10.1128/mbio.00067-24] [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] [Indexed: 02/27/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak took the world by storm due to its rapid global spread and unpredictable disease outcomes. The extraordinary ascension of SARS-CoV-2 to pandemic status motivated a world-wide effort to rapidly develop vaccines that could effectively suppress virus spread and mitigate severe disease. These efforts culminated in the development and deployment of several highly effective vaccines that were heralded as the beginning-of-the-end of the pandemic. However, these successes were short lived due to the unexpected and continuous emergence of more transmissible and immune-evasive SARS-CoV-2 variants. Thus, attention has shifted toward developing novel vaccine platforms that elicit more robust and sustained neutralizing antibody responses. Recent findings by Muñoz-Alía and colleagues address this by combining a live recombinant measles vaccine platform with novel biochemical approaches to generate vaccine candidates that bolster the potency of neutralizing antibody responses against diverse SARS-CoV-2 spike proteins (M. Á. Muñoz-Alía, R. A. Nace, B. Balakrishnan, L. Zhang, et al., mBio 9:e02928-23, 2024, https://doi.org/10.1128/mbio.02928-23).
Collapse
Affiliation(s)
- Daniel J. Salamango
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center, San Antonio, Texas, USA
| |
Collapse
|
29
|
Tortorici MA, Addetia A, Seo AJ, Brown J, Sprouse K, Logue J, Clark E, Franko N, Chu H, Veesler D. Persistent immune imprinting occurs after vaccination with the COVID-19 XBB.1.5 mRNA booster in humans. Immunity 2024; 57:904-911.e4. [PMID: 38490197 DOI: 10.1016/j.immuni.2024.02.016] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and bivalent COVID-19 vaccination primarily recall cross-reactive memory B cells induced by prior Wuhan-Hu-1 spike mRNA vaccination rather than priming Omicron-specific naive B cells. These findings indicate that immune imprinting occurs after repeated Wuhan-Hu-1 spike exposures, but whether it can be overcome remains unclear. To understand the persistence of immune imprinting, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID-19 mRNA vaccine booster. We showed that the XBB.1.5 booster elicited neutralizing antibody responses against current variants that were dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. Therefore, immune imprinting persists after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 booster vaccination, which will need to be considered to guide future vaccination.
Collapse
Affiliation(s)
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaiti Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jenni Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Erica Clark
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
30
|
Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.586409. [PMID: 38617298 PMCID: PMC11014493 DOI: 10.1101/2024.03.31.586409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Middle-East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Most vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts, however, are limited by a poor understanding of antibody responses elicited by infection along with their durability, fine specificity and contribution of distinct S antigenic sites to neutralization. To address this knowledge gap, we analyzed S-directed binding and neutralizing antibody titers in plasma collected from individuals infected with MERS-CoV in 2017-2019 (prior to the COVID-19 pandemic). We observed that binding and neutralizing antibodies peak 1 to 6 weeks after symptom onset/hospitalization, persist for at least 6 months, and broadly neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the RBD, account for most plasma neutralizing activity. Antigenic site mapping revealed that polyclonal plasma antibodies frequently target RBD epitopes, particularly a site exposed irrespective of the S trimer conformation, whereas targeting of S2 subunit epitopes is rare, similar to SARS-CoV-2. Our data reveal in unprecedented details the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
Collapse
Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Kyung Hee University, Seoul, South Korea
| | - Abeer Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| |
Collapse
|
31
|
Trabelsi K, Ben Khalaf N, Ramadan AR, Elsharkawy A, Ashoor D, Chlif S, Boussoffara T, Ben-Ahmed M, Kumar M, Fathallah MD. A novel approach to designing viral precision vaccines applied to SARS-CoV-2. Front Cell Infect Microbiol 2024; 14:1346349. [PMID: 38628551 PMCID: PMC11018900 DOI: 10.3389/fcimb.2024.1346349] [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: 11/29/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.
Collapse
Affiliation(s)
- Khaled Trabelsi
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddin Ben Khalaf
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Amany Elsharkawy
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - Dana Ashoor
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Thouraya Boussoffara
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Melika Ben-Ahmed
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - M-Dahmani Fathallah
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| |
Collapse
|
32
|
Adachi T, Nakamura S, Michishita A, Kawahara D, Yamamoto M, Hamada M, Nakamura Y. RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein. Biochemistry 2024; 63:906-912. [PMID: 38457656 PMCID: PMC10993888 DOI: 10.1021/acs.biochem.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Optimization of aptamers in length and chemistry is crucial for industrial applications. Here, we developed aptamers against the SARS-CoV-2 spike protein and achieved optimization with a deep-learning-based algorithm, RaptGen. We conducted a primer-less SELEX against the receptor binding domain (RBD) of the spike with an RNA/DNA hybrid library, and the resulting sequences were subjected to RaptGen analysis. Based on the sequence profiling by RaptGen, a short truncation aptamer of 26 nucleotides was obtained and further optimized by a chemical modification of relevant nucleotides. The resulting aptamer is bound to RBD not only of SARS-CoV-2 wildtype but also of its variants, SARS-CoV-1, and Middle East respiratory syndrome coronavirus (MERS-CoV). We concluded that the RaptGen-assisted discovery is efficient for developing optimized aptamers.
Collapse
Affiliation(s)
- Tatsuo Adachi
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
| | | | - Akiya Michishita
- Graduate
School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Computational
Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology
(AIST), 3-4-1, Okubo
Shinjuku-ku, Tokyo 169-8555, Japan
| | - Daiki Kawahara
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
| | - Mizuki Yamamoto
- Research
Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Michiaki Hamada
- Graduate
School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Computational
Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology
(AIST), 3-4-1, Okubo
Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshikazu Nakamura
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| |
Collapse
|
33
|
Anzai I, Fujita J, Ono C, Kosaka Y, Miyamoto Y, Shichinohe S, Takada K, Torii S, Taguwa S, Suzuki K, Makino F, Kajita T, Inoue T, Namba K, Watanabe T, Matsuura Y. Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain. Microbiol Spectr 2024; 12:e0365523. [PMID: 38415660 PMCID: PMC10986471 DOI: 10.1128/spectrum.03655-23] [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: 10/11/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Although the global crisis caused by the coronavirus disease 2019 (COVID-19) pandemic is over, the global epidemic of the disease continues. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of COVID-19, initiates infection via the binding of the receptor-binding domain (RBD) of its spike protein to the human angiotensin-converting enzyme II (ACE2) receptor, and this interaction has been the primary target for the development of COVID-19 therapeutics. Here, we identified neutralizing antibodies against SARS-CoV-2 by screening mouse monoclonal antibodies and characterized an antibody, CSW1-1805, that targets a narrow region at the RBD ridge of the spike protein. CSW1-1805 neutralized several variants in vitro and completely protected mice from SARS-CoV-2 infection. Cryo-EM and biochemical analyses revealed that this antibody recognizes the loop region adjacent to the ACE2-binding interface with the RBD in both a receptor-inaccessible "down" state and a receptor-accessible "up" state and could stabilize the RBD conformation in the up-state. CSW1-1805 also showed different binding orientations and complementarity determining region properties compared to other RBD ridge-targeting antibodies with similar binding epitopes. It is important to continuously characterize neutralizing antibodies to address new variants that continue to emerge. Our characterization of this antibody that recognizes the RBD ridge of the spike protein will aid in the development of future neutralizing antibodies.IMPORTANCESARS-CoV-2 cell entry is initiated by the interaction of the viral spike protein with the host cell receptor. Therefore, mechanistic findings regarding receptor recognition by the spike protein help uncover the molecular mechanism of SARS-CoV-2 infection and guide neutralizing antibody development. Here, we characterized a SARS-CoV-2 neutralizing antibody that recognizes an epitope, a loop region adjacent to the receptor-binding interface, that may be involved in the conformational transition of the receptor-binding domain (RBD) of the spike protein from a receptor-inaccessible "down" state into a receptor-accessible "up" state, and also stabilizes the RBD in the up-state. Our mechanistic findings provide new insights into SARS-CoV-2 receptor recognition and guidance for neutralizing antibody development.
Collapse
Grants
- JP16H06429, JP16K21723, JP16H06432 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06429, JP16K21723, JP16H06434 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15042 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP25K000013 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K22630 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP223fa627002, JP22am0401030, JP23fk0108659, JP20jk0210021, JP22gm1610010, JP19fk0108113 Japan Agency for Medical Research and Development (AMED)
- JP223fa627002 Japan Agency for Medical Research and Development (AMED)
- JP19fk0108113, JP20fk0108281, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP21am0101117, JP17pc0101020 Japan Agency for Medical Research and Development (AMED)
- JPMJOP1861 MEXT | Japan Science and Technology Agency (JST)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
Collapse
Affiliation(s)
- Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Chikako Ono
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | | | - Shintaro Shichinohe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shuhei Taguwa
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- JEOL Ltd., Akishima, Tokyo, Japan
| | | | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
34
|
Galeota E, Bevilacqua V, Gobbini A, Gruarin P, Bombaci M, Pesce E, Favalli A, Lombardi A, Vincenti F, Ongaro J, Fabbris T, Curti S, Martinovic M, Toccafondi M, Lorenzo M, Critelli A, Clemente F, Crosti M, Sarnicola ML, Martinelli M, La Sala L, Espadas A, Donnici L, Borghi MO, De Feo T, De Francesco R, Prati D, Meroni PL, Notarbartolo S, Geginat J, Gori A, Bandera A, Abrignani S, Grifantini R. Tracking the immune response profiles elicited by the BNT162b2 vaccine in COVID-19 unexperienced and experienced individuals. Clin Immunol 2024; 261:110164. [PMID: 38417765 DOI: 10.1016/j.clim.2024.110164] [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: 10/02/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Multiple vaccines have been approved to control COVID-19 pandemic, with Pfizer/BioNTech (BNT162b2) being widely used. We conducted a longitudinal analysis of the immune response elicited after three doses of the BNT162b2 vaccine in individuals who have previously experienced SARS-CoV-2 infection and in unexperienced ones. We conducted immunological analyses and single-cell transcriptomics of circulating T and B lymphocytes, combined to CITE-seq or LIBRA-seq, and VDJ-seq. We found that antibody levels against SARS-CoV-2 Spike, NTD and RBD from wild-type, delta and omicron VoCs show comparable dynamics in both vaccination groups, with a peak after the second dose, a decline after six months and a restoration after the booster dose. The antibody neutralization activity was maintained, with lower titers against the omicron variant. Spike-specific memory B cell response was sustained over the vaccination schedule. Clonal analysis revealed that Spike-specific B cells were polyclonal, with a partial clone conservation from natural infection to vaccination. Spike-specific T cell responses were oriented towards effector and effector memory phenotypes, with similar trends in unexperienced and experienced individuals. The CD8 T cell compartment showed a higher clonal expansion and persistence than CD4 T cells. The first two vaccinations doses tended to induce new clones rather than promoting expansion of pre-existing clones. However, we identified a fraction of Spike-specific CD8 T cell clones persisting from natural infection that were boosted by vaccination and clones specifically induced by vaccination. Collectively, our observations revealed a moderate effect of the second dose in enhancing the immune responses elicited after the first vaccination. Differently, we found that a third dose was necessary to restore comparable levels of neutralizing antibodies and Spike-specific T and B cell responses in individuals who experienced a natural SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Eugenia Galeota
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Valeria Bevilacqua
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Andrea Gobbini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Paola Gruarin
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mauro Bombaci
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Andrea Favalli
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Ph.D. Program in Translational and Molecular Medicine, Dottorato in Medicina Molecolare e Traslazionale (DIMET), University of Milan-Bicocca, Monza, Italy
| | - Andrea Lombardi
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Francesca Vincenti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Jessica Ongaro
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Tanya Fabbris
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Serena Curti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Martina Martinovic
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mirco Toccafondi
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariangela Lorenzo
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Angelica Critelli
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Francesca Clemente
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariacristina Crosti
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Lucia Sarnicola
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | | | - Alejandro Espadas
- Laboratory of Transplant Immunology - North Italy Transplant program (NITp) - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Orietta Borghi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy; IRCCS Istituto Auxologico Italiano, Immunorheumatology Research Laboratory, Milan, Italy
| | - Tullia De Feo
- Laboratory of Transplant Immunology - North Italy Transplant program (NITp) - Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Raffaele De Francesco
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Foundation IRCCS Cà Granda Ospedale Maggiore Policlinico of Milan, Italy
| | - Pier Luigi Meroni
- IRCCS Istituto Auxologico Italiano, Immunorheumatology Research Laboratory, Milan, Italy
| | - Samuele Notarbartolo
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Jens Geginat
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Andrea Gori
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Infectious Diseases Unit, Ospedale "Luigi Sacco", Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Centre for Multidisciplinary Research in Health Science (MACH), University of Milano, Milan 20122, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; CheckmAb Srl, Milan, Italy.
| |
Collapse
|
35
|
Costa JNY, Pimentel GJC, Poker JA, Merces L, Paschoalino WJ, Vieira LCS, Castro ACH, Alves WA, Ayres LB, Kubota LT, Santhiago M, Garcia CD, Piazzetta MHO, Gobbi AL, Shimizu FM, Lima RS. Single-Response Duplexing of Electrochemical Label-Free Biosensor from the Same Tag. Adv Healthc Mater 2024; 13:e2303509. [PMID: 38245830 DOI: 10.1002/adhm.202303509] [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: 10/12/2023] [Revised: 01/16/2024] [Indexed: 01/22/2024]
Abstract
Multiplexing is a valuable strategy to boost throughput and improve clinical accuracy. Exploiting the vertical, meshed design of reproducible and low-cost ultra-dense electrochemical chips, the unprecedented single-response multiplexing of typical label-free biosensors is reported. Using a cheap, handheld one-channel workstation and a single redox probe, that is, ferro/ferricyanide, the recognition events taking place on two spatially resolved locations of the same working electrode can be tracked along a single voltammetry scan by collecting the electrochemical signatures of the probe in relation to different quasi-reference electrodes, Au (0 V) and Ag/AgCl ink (+0.2 V). This spatial isolation prevents crosstalk between the redox tags and interferences over functionalization and binding steps, representing an advantage over the existing non-spatially resolved single-response multiplex strategies. As proof of concept, peptide-tethered immunosensors are demonstrated to provide the duplex detection of COVID-19 antibodies, thereby doubling the throughput while achieving 100% accuracy in serum samples. The approach is envisioned to enable broad applications in high-throughput and multi-analyte platforms, as it can be tailored to other biosensing devices and formats.
Collapse
Affiliation(s)
- Juliana N Y Costa
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, 09210-580, Brazil
| | - Gabriel J C Pimentel
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Júlia A Poker
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Leandro Merces
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
| | - Waldemir J Paschoalino
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Luis C S Vieira
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Ana C H Castro
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, 09210-580, Brazil
| | - Wendel A Alves
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, 09210-580, Brazil
| | - Lucas B Ayres
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
| | - Lauro T Kubota
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, 09210-580, Brazil
| | - Murilo Santhiago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Carlos D Garcia
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
| | - Maria H O Piazzetta
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Angelo L Gobbi
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Flávio M Shimizu
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Renato S Lima
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, 09210-580, Brazil
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, São Paulo, 13565-590, Brazil
| |
Collapse
|
36
|
Rexhepaj M, Park YJ, Perruzza L, Asarnow D, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Starr TN, Corti D, Benigni F, Veesler D. Broadly neutralizing antibodies against emerging delta-coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586411. [PMID: 38617231 PMCID: PMC11014491 DOI: 10.1101/2024.03.27.586411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Porcine deltacoronavirus (PDCoV) spillovers were recently detected in children with acute undifferentiated febrile illness, underscoring recurrent zoonoses of divergent coronaviruses. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated human spike (S)-directed monoclonal antibodies from transgenic mice and found that two of them, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryo-electron microscopy structures of PD33 and PD41 in complex with the PDCoV receptor-binding domain and S ectodomain trimer provide a blueprint of the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs inhibit PDCoV by competitively interfering with host APN binding to the PDCoV receptor-binding loops, explaining the mechanism of viral neutralization. PD33 and PD41 are candidates for clinical advancement, which could be stockpiled to prepare for possible future PDCoV outbreaks.
Collapse
Affiliation(s)
- Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisa Perruzza
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Mathew Mccallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Katja Culap
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Giada Leoni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessio Balmelli
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Miles S. Dickinson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jack Taylor Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| |
Collapse
|
37
|
Saha G, Sawmya S, Saha A, Akil MA, Tasnim S, Rahman MS, Rahman MS. PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information. Brief Bioinform 2024; 25:bbae218. [PMID: 38742520 PMCID: PMC11091746 DOI: 10.1093/bib/bbae218] [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: 11/29/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 05/16/2024] Open
Abstract
The dynamic evolution of the severe acute respiratory syndrome coronavirus 2 virus is primarily driven by mutations in its genetic sequence, culminating in the emergence of variants with increased capability to evade host immune responses. Accurate prediction of such mutations is fundamental in mitigating pandemic spread and developing effective control measures. This study introduces a robust and interpretable deep-learning approach called PRIEST. This innovative model leverages time-series viral sequences to foresee potential viral mutations. Our comprehensive experimental evaluations underscore PRIEST's proficiency in accurately predicting immune-evading mutations. Our work represents a substantial step in utilizing deep-learning methodologies for anticipatory viral mutation analysis and pandemic response.
Collapse
Affiliation(s)
- Gourab Saha
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Shashata Sawmya
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Arpita Saha
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md Ajwad Akil
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Sadia Tasnim
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - M Sohel Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| |
Collapse
|
38
|
Monteiro MES, Lechuga GC, Napoleão-Pêgo P, Carvalho JPRS, Gomes LR, Morel CM, Provance DW, De-Simone SG. Humoral Immune Response to SARS-CoV-2 Spike Protein Receptor-Binding Motif Linear Epitopes. Vaccines (Basel) 2024; 12:342. [PMID: 38675725 PMCID: PMC11055068 DOI: 10.3390/vaccines12040342] [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: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
The worldwide spread of SARS-CoV-2 has led to a significant economic and social burden on a global scale. Even though the pandemic has concluded, apprehension remains regarding the emergence of highly transmissible variants capable of evading immunity induced by either vaccination or prior infection. The success of viral penetration is due to the specific amino acid residues of the receptor-binding motif (RBM) involved in viral attachment. This region interacts with the cellular receptor ACE2, triggering a neutralizing antibody (nAb) response. In this study, we evaluated serum immunogenicity from individuals who received either a single dose or a combination of different vaccines against the original SARS-CoV-2 strain and a mutated linear RBM. Despite a modest antibody response to wild-type SARS-CoV-2 RBM, the Omicron variants exhibit four mutations in the RBM (S477N, T478K, E484A, and F486V) that result in even lower antibody titers. The primary immune responses observed were directed toward IgA and IgG. While nAbs typically target the RBD, our investigation has unveiled reduced seroreactivity within the RBD's crucial subregion, the RBM. This deficiency may have implications for the generation of protective nAbs. An evaluation of S1WT and S2WT RBM peptides binding to nAbs using microscale thermophoresis revealed a higher affinity (35 nM) for the S2WT sequence (GSTPCNGVEGFNCYF), which includes the FNCY patch. Our findings suggest that the linear RBM of SARS-CoV-2 is not an immunodominant region in vaccinated individuals. Comprehending the intricate dynamics of the humoral response, its interplay with viral evolution, and host genetics is crucial for formulating effective vaccination strategies, targeting not only SARS-CoV-2 but also anticipating potential future coronaviruses.
Collapse
Affiliation(s)
- Maria E. S. Monteiro
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - João P. R. S. Carvalho
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
| | - Larissa R. Gomes
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - Carlos M. Morel
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - David W. Provance
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
| |
Collapse
|
39
|
Lebedin M, Ratswohl C, Garg A, Schips M, García CV, Spatt L, Thibeault C, Obermayer B, Weiner J, Velásquez IM, Gerhard C, Stubbemann P, Hanitsch LG, Pischon T, Witzenrath M, Sander LE, Kurth F, Meyer-Hermann M, de la Rosa K. Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses. iScience 2024; 27:109330. [PMID: 38496296 PMCID: PMC10940809 DOI: 10.1016/j.isci.2024.109330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/25/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Identifying immune modulators that impact neutralizing antibody responses against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is of great relevance. We postulated that high serum concentrations of soluble angiotensin-converting enzyme 2 (sACE2) might mask the spike and interfere with antibody maturation toward the SARS-CoV-2-receptor-binding motif (RBM). We tested 717 longitudinal samples from 295 COVID-19 patients and showed a 2- to 10-fold increase of enzymatically active sACE2 (a-sACE2), with up to 1 μg/mL total sACE2 in moderate and severe patients. Fifty percent of COVID-19 sera inhibited ACE2 activity, in contrast to 1.3% of healthy donors and 4% of non-COVID-19 pneumonia patients. A mild inverse correlation of a-sACE2 with RBM-directed serum antibodies was observed. In silico, we show that sACE2 concentrations measured in COVID-19 sera can disrupt germinal center formation and inhibit timely production of high-affinity antibodies. We suggest that sACE2 is a biomarker for COVID-19 and that soluble receptors may contribute to immune suppression informing vaccine design.
Collapse
Affiliation(s)
- Mikhail Lebedin
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Ratswohl
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Free University of Berlin, Department of Biology, Chemistry and Pharmacy, 14195 Berlin, Berlin, Germany
| | - Amar Garg
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Schips
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Clara Vázquez García
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa Spatt
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - January Weiner
- Core Unit Bioinformatics, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ilais Moreno Velásquez
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Cathrin Gerhard
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Paula Stubbemann
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Leif-Gunnar Hanitsch
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tobias Pischon
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Biobank Technology Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
| | - Michael Meyer-Hermann
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kathrin de la Rosa
- Max-Delbück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| |
Collapse
|
40
|
Chao CW, Sprouse KR, Miranda MC, Catanzaro NJ, Hubbard ML, Addetia A, Stewart C, Brown JT, Dosey A, Valdez A, Ravichandran R, Hendricks GG, Ahlrichs M, Dobbins C, Hand A, Treichel C, Willoughby I, Walls AC, McGuire AT, Leaf EM, Baric RS, Schäfer A, Veesler D, King NP. Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584735. [PMID: 38558973 PMCID: PMC10979991 DOI: 10.1101/2024.03.13.584735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
Collapse
Affiliation(s)
- Cara W Chao
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Grace G Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Isabelle Willoughby
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Leaf
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
41
|
Inchauste L, Nurtop E, Brisbarre N, Ninove L, Gallian P, de Lamballerie X, Priet S. Exploring cell-free assays for COVID-19 serosurvey. Sci Rep 2024; 14:6096. [PMID: 38480769 PMCID: PMC10938000 DOI: 10.1038/s41598-024-55852-6] [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: 02/14/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Serosurveys to monitor immunity toward COVID-19 in the population are primarily performed using an ELISA to screen samples for SARS-CoV-2 antibodies, followed by confirmation by a virus neutralization test, which is considered the Gold Standard. However, virus neutralization test may not be feasible for some laboratories because of the requirement for specific facilities and trained personnel. In an attempt to address this limitation, we evaluated three cell-free methods as potential alternatives for assessing SARS-CoV-2 seroprevalence in human population from plasma. We report the establishment of two inhibition ELISAs designed to detect anti-Spike RBD IgG antibodies and a microsphere quantitative suspension array technology assay, based on the Luminex xMAP platform, to measure the presence of antibodies against various SARS-CoV-2 antigens, including anti-RBD. These methods were also compared to a commercial chemiluminescent immunoassay designed for anti-RBD antibodies detection and to the combined ELISA + virus neutralization test strategy. These cell-free assays performed equally to estimate the percentage of positive and negative samples and could be used to determine the prevalence of SARS-CoV-2 antibodies in human population, at least in cohort with high-expected prevalence, without the use of seroneutralization assay.
Collapse
Affiliation(s)
- Lucia Inchauste
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Elif Nurtop
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Nadège Brisbarre
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Établissement Français du Sang Provence Alpes Côte d'Azur et Corse, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Pierre Gallian
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Établissement Français du Sang, La Plaine Saint-Denis, Saint-Denis, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Stéphane Priet
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
| |
Collapse
|
42
|
Clever S, Limpinsel L, Meyer zu Natrup C, Schünemann LM, Beythien G, Rosiak M, Hülskötter K, Gregor KM, Tuchel T, Kalodimou G, Freudenstein A, Kumar S, Baumgärtner W, Sutter G, Tscherne A, Volz A. Single MVA-SARS-2-ST/N Vaccination Rapidly Protects K18-hACE2 Mice against a Lethal SARS-CoV-2 Challenge Infection. Viruses 2024; 16:417. [PMID: 38543782 PMCID: PMC10974247 DOI: 10.3390/v16030417] [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: 02/09/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
The sudden emergence of SARS-CoV-2 demonstrates the need for new vaccines that rapidly protect in the case of an emergency. In this study, we developed a recombinant MVA vaccine co-expressing SARS-CoV-2 prefusion-stabilized spike protein (ST) and SARS-CoV-2 nucleoprotein (N, MVA-SARS-2-ST/N) as an approach to further improve vaccine-induced immunogenicity and efficacy. Single MVA-SARS-2-ST/N vaccination in K18-hACE2 mice induced robust protection against lethal respiratory SARS-CoV-2 challenge infection 28 days later. The protective outcome of MVA-SARS-2-ST/N vaccination correlated with the activation of SARS-CoV-2-neutralizing antibodies (nABs) and substantial amounts of SARS-CoV-2-specific T cells especially in the lung of MVA-SARS-2-ST/N-vaccinated mice. Emergency vaccination with MVA-SARS-2-ST/N just 2 days before lethal SARS-CoV-2 challenge infection resulted in a delayed onset of clinical disease outcome in these mice and increased titers of nAB or SARS-CoV-2-specific T cells in the spleen and lung. These data highlight the potential of a multivalent COVID-19 vaccine co-expressing S- and N-protein, which further contributes to the development of rapidly protective vaccination strategies against emerging pathogens.
Collapse
Affiliation(s)
- Sabrina Clever
- Institute of Virology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (S.C.); (C.M.z.N.); (L.-M.S.)
| | - Leonard Limpinsel
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Christian Meyer zu Natrup
- Institute of Virology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (S.C.); (C.M.z.N.); (L.-M.S.)
| | - Lisa-Marie Schünemann
- Institute of Virology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (S.C.); (C.M.z.N.); (L.-M.S.)
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (G.B.); (M.R.); (K.H.); (K.M.G.); (W.B.)
| | - Malgorzata Rosiak
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (G.B.); (M.R.); (K.H.); (K.M.G.); (W.B.)
| | - Kirsten Hülskötter
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (G.B.); (M.R.); (K.H.); (K.M.G.); (W.B.)
| | - Katharina Manuela Gregor
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (G.B.); (M.R.); (K.H.); (K.M.G.); (W.B.)
| | - Tamara Tuchel
- Institute of Virology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (S.C.); (C.M.z.N.); (L.-M.S.)
| | - Georgia Kalodimou
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Astrid Freudenstein
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Satendra Kumar
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (G.B.); (M.R.); (K.H.); (K.M.G.); (W.B.)
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Alina Tscherne
- Division of Virology, Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany; (L.L.); (G.K.); (A.F.); (S.K.); (G.S.); (A.T.)
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany; (S.C.); (C.M.z.N.); (L.-M.S.)
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Titova E, Kan VW, Lozy T, Ip A, Shier K, Prakash VP, Starolis M, Ansari S, Goldgirsh K, Kim S, Pelliccia MC, Mccutchen A, Megalla M, Gunning TS, Kaufman HW, Meyer WA, Perlin DS. Humoral and cellular immune responses against SARS-CoV-2 post-vaccination in immunocompetent and immunocompromised cancer populations. Microbiol Spectr 2024; 12:e0205023. [PMID: 38353557 PMCID: PMC10913742 DOI: 10.1128/spectrum.02050-23] [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: 05/17/2023] [Accepted: 01/04/2024] [Indexed: 03/06/2024] Open
Abstract
Cancer patients are at risk for severe coronavirus disease 2019 (COVID-19) outcomes due to impaired immune responses. However, the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is inadequately characterized in this population. We hypothesized that cancer vs non-cancer individuals would mount less robust humoral and/or cellular vaccine-induced immune SARS-CoV-2 responses. Receptor binding domain (RBD) and SARS-CoV-2 spike protein antibody levels and T-cell responses were assessed in immunocompetent individuals with no underlying disorders (n = 479) and immunocompromised individuals (n = 115). All 594 individuals were vaccinated and of varying COVID-19 statuses (i.e., not known to have been infected, previously infected, or "Long-COVID"). Among immunocompromised individuals, 59% (n = 68) had an underlying hematologic malignancy; of those, 46% (n = 31) of individuals received cancer treatment <30 days prior to study blood collection. Ninety-eight percentage (n = 469) of immunocompetent and 81% (n = 93) of immunocompromised individuals had elevated RBD antibody titers (>1,000 U/mL), and of these, 60% (n = 281) and 44% (n = 41), respectively, also had elevated T-cell responses. Composite T-cell responses were higher in individuals previously infected with SARS-CoV-2 or those diagnosed with Long-COVID compared to uninfected individuals. T-cell responses varied between immunocompetent vs carcinoma (n = 12) cohorts (P < 0.01) but not in immunocompetent vs hematologic malignancy cohorts. Most SARS-CoV-2 vaccinated individuals mounted robust cellular and/or humoral responses, though higher immunogenicity was observed among the immunocompetent compared to cancer populations. The study suggests B-cell targeted therapies suppress antibody responses, but not T-cell responses, to SARS-CoV-2 vaccination. Thus, vaccination continues to be an effective way to induce humoral and cellular immune responses as a likely key preventive measure against infection and/or subsequent more severe adverse outcomes. IMPORTANCE The study was prompted by a desire to better assess the immune status of patients among our cancer host cohort, one of the largest in the New York metropolitan region. Hackensack Meridian Health is the largest healthcare system in New Jersey and cared for more than 75,000 coronavirus disease 2019 patients in its hospitals. The John Theurer Cancer Center sees more than 35,000 new cancer patients a year and performs more than 500 hematopoietic stem cell transplants. As a result, the work was undertaken to assess the effectiveness of vaccination in inducing humoral and cellular responses within this demographic.
Collapse
Affiliation(s)
- Elizabeth Titova
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Veronica W. Kan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Tara Lozy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Andrew Ip
- John Theurer Cancer Center, Hackensack, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | | | | | | | - Sara Ansari
- Quest Diagnostics, Secaucus, New Jersey, USA
| | - Kira Goldgirsh
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Seoyeon Kim
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Michael C. Pelliccia
- John Theurer Cancer Center, Hackensack, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Aamirah Mccutchen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Martinus Megalla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Thomas S. Gunning
- John Theurer Cancer Center, Hackensack, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | | | | | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| |
Collapse
|
45
|
Patel DR, Minns AM, Sim DG, Field CJ, Kerr AE, Heinly TA, Luley EH, Rossi RM, Bator CM, Moustafa IM, Norton EB, Hafenstein SL, Lindner SE, Sutton TC. Intranasal SARS-CoV-2 RBD decorated nanoparticle vaccine enhances viral clearance in the Syrian hamster model. Microbiol Spectr 2024; 12:e0499822. [PMID: 38334387 PMCID: PMC10923206 DOI: 10.1128/spectrum.04998-22] [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: 12/05/2022] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Multiple vaccines have been developed and licensed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). While these vaccines reduce disease severity, they do not prevent infection. To prevent infection and limit transmission, vaccines must be developed that induce immunity in the respiratory tract. Therefore, we performed proof-of-principle studies with an intranasal nanoparticle vaccine against SARS-CoV-2. The vaccine candidate consisted of the self-assembling 60-subunit I3-01 protein scaffold covalently decorated with the SARS-CoV-2 receptor-binding domain (RBD) using the SpyCatcher-SpyTag system. We verified the intended antigen display features by reconstructing the I3-01 scaffold to 3.4 A using cryogenicelectron microscopy. Using this RBD-grafted SpyCage scaffold (RBD + SpyCage), we performed two intranasal vaccination studies in the "gold-standard" pre-clinical Syrian hamster model. The initial study focused on assessing the immunogenicity of RBD + SpyCage combined with the LTA1 intranasal adjuvant. These studies showed RBD + SpyCage vaccination induced an antibody response that promoted viral clearance but did not prevent infection. Inclusion of the LTA1 adjuvant enhanced the magnitude of the antibody response but did not enhance protection. Thus, in an expanded study, in the absence of an intranasal adjuvant, we evaluated if covalent bonding of RBD to the scaffold was required to induce an antibody response. Covalent grafting of RBD was required for the vaccine to be immunogenic, and animals vaccinated with RBD + SpyCage more rapidly cleared SARS-CoV-2 from both the upper and lower respiratory tract. These findings demonstrate the intranasal SpyCage vaccine platform can induce protection against SARS-CoV-2 and, with additional modifications to improve immunogenicity, is a versatile platform for the development of intranasal vaccines targeting respiratory pathogens.IMPORTANCEDespite the availability of efficacious COVID vaccines that reduce disease severity, SARS-CoV-2 continues to spread. To limit SARS-CoV-2 transmission, the next generation of vaccines must induce immunity in the mucosa of the upper respiratory tract. Therefore, we performed proof-of-principle, intranasal vaccination studies with a recombinant protein nanoparticle scaffold, SpyCage, decorated with the RBD of the S protein (SpyCage + RBD). We show that SpyCage + RBD was immunogenic and enhanced SARS-CoV-2 clearance from the nose and lungs of Syrian hamsters. Moreover, covalent grafting of the RBD to the scaffold was required to induce an immune response when given via the intranasal route. These proof-of-concept findings indicate that with further enhancements to immunogenicity (e.g., adjuvant incorporation and antigen optimization), the SpyCage scaffold has potential as a versatile, intranasal vaccine platform for respiratory pathogens.
Collapse
Affiliation(s)
- Devanshi R. Patel
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Allen M. Minns
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Center for Malaria Research, University Park, Pennsylvania, USA
| | - Derek G. Sim
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Cassandra J. Field
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abigail E. Kerr
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Talia A. Heinly
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Erin H. Luley
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Randall M. Rossi
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carol M. Bator
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Elizabeth B. Norton
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, USA
| | - Susan L. Hafenstein
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott E. Lindner
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Center for Malaria Research, University Park, Pennsylvania, USA
| | - Troy C. Sutton
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
46
|
Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Development of a potent recombinant scFv antibody against the SARS-CoV-2 by in-depth bioinformatics study: Paving the way for vaccine/diagnostics development. Comput Biol Med 2024; 170:108091. [PMID: 38295473 DOI: 10.1016/j.compbiomed.2024.108091] [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: 05/09/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND The SARS-CoV-2 has led to a worldwide disaster. Thus, developing prophylactics/therapeutics is required to overcome this public health issue. Among these, producing the anti-SARS-CoV-2 single-chain variable fragment (scFv) antibodies has attracted a significant attention. Accordingly, this study aims to address this question: Is it possible to bioinformatics-based design of a potent anti-SARS-CoV-2 scFv as an alternative to current production approaches? METHOD Using the complexed SARS-CoV-2 spike-antibodies, two sets analyses were performed: (1) B-cell epitopes (BCEs) prediction in the spike receptor-binding domain (RBD) region as a parameter for antibody screening; (2) the computational analysis of antibodies variable domains (VH/VL). Based on these primary screenings, and docking/binding affinity rating, one antibody was selected. The protein-protein interactions (PPIs) among the selected antibody-epitope complex were predicted and its epitope conservancy was also evaluated. Thereafter, some elements were added to the final scFv: (1) the PelB signal peptide; (2) a GSGGGGS linker to connect the VH-VL. Finally, this scFv was analyzed/optimized using various web servers. RESULTS Among the antibody library, only one met the various criteria for being an efficient scFv candidate. Moreover, no interaction was predicted between its paratope and RBD hot-spot residues of SARS-CoV-2 variants-of-Concern (VOCs). CONCLUSIONS Herein, a step-by-step bioinformatics platform has been introduced to bypass some barriers of traditional antibody production approaches. Based on existing literature, the current study is one of the pioneer works in the field of bioinformatics-based scFv production. This scFv may be a good candidate for diagnostics/therapeutics design against the SARS-CoV-2 as an emerging aggressive pathogen.
Collapse
Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| |
Collapse
|
47
|
Costa Rocha VP, Souza Machado BA, Barreto BC, Quadros HC, Santana Fernandes AM, Lima EDS, Bandeira ME, Meira CS, Moraes dos Santos Fonseca L, Erasmus J, Khandhar A, Berglund P, Reed S, José da Silva Badaró R, Pereira Soares MB. A polyvalent RNA vaccine reduces the immune imprinting phenotype in mice and induces neutralizing antibodies against omicron SARS-CoV-2. Heliyon 2024; 10:e25539. [PMID: 38370238 PMCID: PMC10869778 DOI: 10.1016/j.heliyon.2024.e25539] [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: 12/02/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Immune imprinting is now evident in COVID-19 vaccinated people. This phenomenon may impair the development of effective neutralizing antibodies against variants of concern (VoCs), mainly Omicron and its subvariants. Consequently, the boost doses with bivalent vaccines have not shown a significant gain of function regarding the neutralization of Omicron. The approach to design COVID-19 vaccines must be revised to improve the effectiveness against VoCs. Here, we took advantage of the self-amplifying characteristic of RepRNA and developed a polyvalent formulation composed of mRNA from five VoCs. LION/RepRNA Polyvalent induced neutralizing antibodies in mice previously immunized with LION/RepRNA D614G and reduced the imprinted phenotype associated with low neutralization capacity of Omicron B.1.1.529 pseudoviruses. The polyvalent vaccine can be a strategy to handle the low neutralization of Omicron VoC, despite booster doses with either monovalent or bivalent vaccines.
Collapse
Affiliation(s)
- Vinicius Pinto Costa Rocha
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- University Center SENAI CIMATEC, Salvador, Bahia, Brazil
| | | | - Helenita Costa Quadros
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | | | - Eduarda dos Santos Lima
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Mariana Evangelista Bandeira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Cássio Santana Meira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | | | | | | | | | | | - Roberto José da Silva Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Milena Botelho Pereira Soares
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| |
Collapse
|
48
|
Hsieh CL, Leist SR, Miller EH, Zhou L, Powers JM, Tse AL, Wang A, West A, Zweigart MR, Schisler JC, Jangra RK, Chandran K, Baric RS, McLellan JS. Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge. Nat Commun 2024; 15:1553. [PMID: 38378768 PMCID: PMC10879192 DOI: 10.1038/s41467-024-45404-x] [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: 08/25/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.
Collapse
Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine-Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, 71103, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
49
|
Wang Z, Huang AS, Tang L, Wang J, Wang G. Microfluidic-assisted single-cell RNA sequencing facilitates the development of neutralizing monoclonal antibodies against SARS-CoV-2. LAB ON A CHIP 2024; 24:642-657. [PMID: 38165771 DOI: 10.1039/d3lc00749a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
As a class of antibodies that specifically bind to a virus and block its entry, neutralizing monoclonal antibodies (neutralizing mAbs) have been recognized as a top choice for combating COVID-19 due to their high specificity and efficacy in treating serious infections. Although conventional approaches for neutralizing mAb development have been optimized for decades, there is an urgent need for workflows with higher efficiency due to time-sensitive concerns, including the high mutation rate of SARS-CoV-2. One promising approach is the identification of neutralizing mAb candidates via single-cell RNA sequencing (RNA-seq), as each B cell has a unique transcript sequence corresponding to its secreted antibody. The state-of-the-art high-throughput single-cell sequencing technologies, which have been greatly facilitated by advances in microfluidics, have greatly accelerated the process of neutralizing mAb development. Here, we provide an overview of the general procedures for high-throughput single-cell RNA-seq enabled by breakthroughs in droplet microfluidics, introduce revolutionary approaches that combine single-cell RNA-seq to facilitate the development of neutralizing mAbs against SARS-CoV-2, and outline future steps that need to be taken to further improve development strategies for effective treatments against infectious diseases.
Collapse
Affiliation(s)
- Ziwei Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Amelia Siqi Huang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Lingfang Tang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guanbo Wang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|