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Martviset P, Thanongsaksrikul J, Geadkaew-Krenc A, Chaimon S, Glab-Ampai K, Chaibangyang W, Sornchuer P, Srimanote P, Ruangtong J, Prathaphan P, Taechadamrongtham T, Torungkitmangmi N, Sanannam B, Gordon CN, Thongsepee N, Pankao V, Chantree P. Production and immunological characterization of the novel single-chain variable fragment (scFv) antibodies against the epitopes on Opisthorchis viverrini cathepsin F (OvCatF). Acta Trop 2024; 254:107199. [PMID: 38552996 DOI: 10.1016/j.actatropica.2024.107199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Opisthorchis viverrini infection is a significant health problem in several countries, especially Southeast Asia. The infection causes acute gastro-hepatic symptoms and also long-term infection leading to carcinogenesis of an aggressive bile duct cancer (cholangiocarcinoma; CCA). Hence, the early diagnosis of O. viverrini infection could be the way out of this situation. Still, stool examination by microscopic-based methods, the current diagnostic procedure is restricted by low parasite egg numbers in the specimen and unprofessional laboratorians. The immunological procedure provides a better chance for diagnosis of the infection. Hence, this study aims to produce single-chain variable fragment (scFv) antibodies for use as a diagnostic tool for O. viverrini infection. METHODS This study uses phage display technologies to develop the scFv antibodies against O. viverrini cathepsin F (OvCatF). The OvCatF-deduced amino acid sequence was analyzed and predicted for B-cell epitopes used for short peptide synthesis. The synthetic peptides were used to screen the phage library simultaneously with OvCatF recombinant protein (rOvCatF). The potentiated phages were collected, rescued, and reassembled in XL1-blue Escherichia coli (E. coli) as a propagative host. The positive clones of phagemids were isolated, and the single-chain variable (scFv) fragments were sequenced, computationally predicted, and molecular docked. The complete scFv fragments were digested from the phagemid, subcloned into the pOPE101 expression vector, and expressed in XL1-blue E. coli. Indirect ELISA and Western analysis were used to verify the detection efficiency. RESULTS The scFv phages specific to OvCatF were successfully isolated, subcloned, and produced as a recombinant protein. The recombinant scFv antibodies were purified and refolded to make functional scFv. The evaluation of specific recognition of the particular epitopes and detection limit results by both computational and laboratory performances demonstrated that all three recombinant scFv antibodies against OvCatF could bind specifically to rOvCatF, and the lowest detection concentration in this study was only one hundred nanograms. CONCLUSION Our produced scFv antibodies will be the potential candidates for developing a practical diagnostic procedure for O. viverrini infection in humans in the future.
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Affiliation(s)
- Pongsakorn Martviset
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Jeeraphong Thanongsaksrikul
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Amornrat Geadkaew-Krenc
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Salisa Chaimon
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Kantaphon Glab-Ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanlapa Chaibangyang
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Phornphan Sornchuer
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand
| | - Potjanee Srimanote
- Graduate Studies in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Jittiporn Ruangtong
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand
| | - Parisa Prathaphan
- Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | | | - Nattaya Torungkitmangmi
- Graduate Program in Biochemistry and Molecular Biology, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Bumpenporn Sanannam
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | | | - Nattaya Thongsepee
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Viriya Pankao
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Pathanin Chantree
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; Thammasat University Research Unit in Nutraceuticals and Food Safety, Thammasat University, Pathumthani, Thailand; Graduate Program in Applied Biosciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand.
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Heidarnejad F, Namvar A, Sadat SM, Pordanjani PM, Rezaei F, Namdari H, Arjmand S, Bolhassani A. In silico designing of novel epitope-based peptide vaccines against HIV-1. Biotechnol Lett 2024; 46:315-354. [PMID: 38403788 DOI: 10.1007/s10529-023-03464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/16/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
The HIV-1 virus has been regarded as a catastrophe for human well-being. The global incidence of HIV-1-infected individuals is increasing. Hence, development of effective immunostimulatory molecules has recently attracted an increasing attention in the field of vaccine design against HIV-1 infection. In this study, we explored the impacts of CD40L and IFN-γ as immunostimulatory adjuvants for our candidate HIV-1 Nef vaccine in human and mouse using immunoinformatics analyses. Overall, 18 IFN-γ-based vaccine constructs (9 constructs in human and 9 constructs in mouse), and 18 CD40L-based vaccine constructs (9 constructs in human and 9 constructs in mouse) were designed. To find immunogenic epitopes, important characteristics of each component (e.g., MHC-I and MHC-II binding, and peptide-MHC-I/MHC-II molecular docking) were determined. Then, the selected epitopes were applied to create multiepitope constructs. Finally, the physicochemical properties, linear and discontinuous B cell epitopes, and molecular interaction between the 3D structure of each construct and CD40, IFN-γ receptor or toll-like receptors (TLRs) were predicted. Our data showed that the full-length CD40L and IFN-γ linked to the N-terminal region of Nef were capable of inducing more effective immune response than multiepitope vaccine constructs. Moreover, molecular docking of the non-allergenic full-length- and epitope-based CD40L and IFN-γ constructs to their cognate receptors, CD40 and IFN-γ receptors, and TLRs 4 and 5 in mouse were more potent than in human. Generally, these findings suggest that the full forms of these adjuvants could be more efficient for improvement of HIV-1 Nef vaccine candidate compared to the designed multiepitope-based constructs.
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Affiliation(s)
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rezaei
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Haideh Namdari
- Iranian Tissue Bank Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Arjmand
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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3
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Li Q, Ma X, Shen Y, Dai J, Nian X, Shang X, Chen J, Wubshet AK, Zhang J, Zheng H. Chimeric Porcine Parvovirus VP2 Virus-like Particles with Epitopes of South African Serotype 2 Foot-and-Mouth Disease Virus Elicits Specific Humoral and Cellular Responses in Mice. Viruses 2024; 16:621. [PMID: 38675963 PMCID: PMC11054767 DOI: 10.3390/v16040621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/30/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Southern Africa Territories 2 (SAT2) foot-and-mouth disease (FMD) has crossed long-standing regional boundaries in recent years and entered the Middle East. However, the existing vaccines offer poor cross-protection against the circulating strains in the field. Therefore, there is an urgent need for an alternative design approach for vaccines in anticipation of a pandemic of SAT2 Foot-and-mouth disease virus (FMDV). The porcine parvovirus (PPV) VP2 protein can embed exogenous epitopes into the four loops on its surface, assemble into virus-like particles (VLPs), and induce antibodies and cytokines to PPV and the exogenous epitope. In this study, chimeric porcine parvovirus VP2 VLPs (chimeric PPV-SAT2-VLPs) expressing the T-and/or B-cell epitopes of the structural protein VP1 of FMDV SAT2 were produced using the recombinant pFastBac™ Dual vector of baculoviruses in Sf9 and HF cells We used the Bac-to-Bac system to construct the recombinant baculoviruses. The VP2-VLP--SAT2 chimeras displayed chimeric T-cell epitope (amino acids 21-40 of VP1) and/or the B-cell epitope (amino acids 135-174) of SAT FMDV VP1 by substitution of the corresponding regions at the N terminus (amino acids 2-23) and/or loop 2 and/or loop 4 of the PPV VP2 protein, respectively. In mice, the chimeric PPV-SAT2-VLPs induced specific antibodies against PPV and the VP1 protein of SAT2 FMDV. The VP2-VLP-SAT2 chimeras induced specific antibodies to PPV and the VP1 protein specific epitopes of FMDV SAT2. In this study, as a proof-of-concept, successfully generated chimeric PPV-VP2 VLPs expressing epitopes of the structural protein VP1 of FMDV SAT2 that has a potential to prevent FMDV SAT2 and PPV infection in pigs.
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MESH Headings
- Animals
- Foot-and-Mouth Disease Virus/immunology
- Foot-and-Mouth Disease Virus/genetics
- Mice
- Foot-and-Mouth Disease/immunology
- Foot-and-Mouth Disease/prevention & control
- Foot-and-Mouth Disease/virology
- Capsid Proteins/immunology
- Capsid Proteins/genetics
- Parvovirus, Porcine/immunology
- Parvovirus, Porcine/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Viral Vaccines/immunology
- Viral Vaccines/genetics
- Vaccines, Virus-Like Particle/immunology
- Vaccines, Virus-Like Particle/genetics
- Swine
- Immunity, Humoral
- Immunity, Cellular
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/genetics
- Serogroup
- Mice, Inbred BALB C
- Female
- Epitopes/immunology
- Epitopes/genetics
- Sf9 Cells
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Antigens, Viral
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Affiliation(s)
- Qian Li
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Xusheng Ma
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Yaner Shen
- China Agricultural Vet Biologyand Technology Co., Ltd., Lanzhou 730046, China;
| | - Junfei Dai
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
| | - Xiaofeng Nian
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
| | - Xiaofen Shang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
| | - Jiao Chen
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
| | - Ashenafi Kiros Wubshet
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
| | - Jie Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, College of Veterinary Medicine, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (Q.L.); (X.M.); (J.D.); (X.S.); (J.C.); (A.K.W.)
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
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4
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Arega AM, Dhal AK, Pattanaik KP, Nayak S, Mahapatra RK. An Immunoinformatics-Based Study of Mycobacterium tuberculosis Region of Difference-2 Uncharacterized Protein (Rv1987) as a Potential Subunit Vaccine Candidate for Preliminary Ex Vivo Analysis. Appl Biochem Biotechnol 2024; 196:2367-2395. [PMID: 37498378 DOI: 10.1007/s12010-023-04658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 07/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is the pathogen that causes tuberculosis and develops resistance to many of the existing drugs. The sole licensed TB vaccine, BCG, is unable to provide a comprehensive defense. So, it is crucial to maintain the immunological response to eliminate tuberculosis. Our previous in silico study reported five uncharacterized proteins as potential vaccine antigens. In this article, we considered the uncharacterized Mtb H37Rv regions of difference (RD-2) Rv1987 protein as a promising vaccine candidate. The vaccine quality of the protein was analyzed using reverse vaccinology and immunoinformatics-based quality-checking parameters followed by an ex vivo preliminary investigation. In silico analysis of Rv1987 protein predicted it as surface localized, secretory, single helix, antigenic, non-allergenic, and non-homologous to the host protein. Immunoinformatics analysis of Rv1987 by CD4 + and CD8 + T-cells via MHC-I and MHC-II binding affinity and presence of B-cell epitope predicted its immunogenicity. The docked complex analysis of the 3D model structure of the protein with immune cell receptor TLR-4 revealed the protein's capability for potential interaction. Furthermore, the target protein-encoded gene Rv1987 was cloned, over-expressed, purified, and analyzed by mass spectrometry (MS) to report the target peptides. The qRT-PCR gene expression analysis shows that it is capable of activating macrophages and significantly increasing the production of a number of key cytokines (TNF-α, IL-1β, and IL-10). Our in-silico analysis and ex vivo preliminary investigations revealed the immunogenic potential of the target protein. These findings suggest that the Rv1987 be undertaken as a potent subunit vaccine antigen and that further animal model immuno-modulation studies would boost the novel TB vaccine discovery and/or BCG vaccine supplement pipeline.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
- National Veterinary Institute, Debre Zeit, Ethiopia
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
| | | | - Sasmita Nayak
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
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5
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Yisimayi A, Song W, Wang J, Jian F, Yu Y, Chen X, Xu Y, Yang S, Niu X, Xiao T, Wang J, Zhao L, Sun H, An R, Zhang N, Wang Y, Wang P, Yu L, Lv Z, Gu Q, Shao F, Jin R, Shen Z, Xie XS, Wang Y, Cao Y. Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting. Nature 2024; 625:148-156. [PMID: 37993710 PMCID: PMC10764275 DOI: 10.1038/s41586-023-06753-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by vaccination based on the ancestral (hereafter referred to as WT) strain would compromise the antibody response to Omicron-based boosters1-5. Vaccination strategies to counter immune imprinting are critically needed. Here we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. In mice, the efficacy of single Omicron boosting is heavily limited when using variants that are antigenically distinct from WT-such as the XBB variant-and this concerning situation could be mitigated by a second Omicron booster. Similarly, in humans, repeated Omicron infections could alleviate WT vaccination-induced immune imprinting and generate broad neutralization responses in both plasma and nasal mucosa. Notably, deep mutational scanning-based epitope characterization of 781 receptor-binding domain (RBD)-targeting monoclonal antibodies isolated from repeated Omicron infection revealed that double Omicron exposure could induce a large proportion of matured Omicron-specific antibodies that have distinct RBD epitopes to WT-induced antibodies. Consequently, immune imprinting was largely mitigated, and the bias towards non-neutralizing epitopes observed in single Omicron exposures was restored. On the basis of the deep mutational scanning profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated that these mutations could further boost the immune-evasion capability of XBB.1.5 while maintaining high ACE2-binding affinity. Our findings suggest that the WT component should be abandoned when updating COVID-19 vaccines, and individuals without prior Omicron exposure should receive two updated vaccine boosters.
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Affiliation(s)
- Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | | | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Yanli Xu
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | - Ran An
- Changping Laboratory, Beijing, P. R. China
| | - Na Zhang
- Changping Laboratory, Beijing, P. R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P. R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P. R. China
| | | | - Zhe Lv
- Sinovac Biotech, Beijing, P. R. China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China
- Institute of Medical Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, P. R. China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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6
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Wang Q, Guo Y, Liu L, Schwanz LT, Li Z, Nair MS, Ho J, Zhang RM, Iketani S, Yu J, Huang Y, Qu Y, Valdez R, Lauring AS, Huang Y, Gordon A, Wang HH, Liu L, Ho DD. Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike. Nature 2023; 624:639-644. [PMID: 37871613 DOI: 10.1038/s41586-023-06750-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant, BA.2.86, has emerged and spread to numerous countries worldwide, raising alarm because its spike protein contains 34 additional mutations compared with its BA.2 predecessor1. We examined its antigenicity using human sera and monoclonal antibodies (mAbs). Reassuringly, BA.2.86 was no more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from people who had XBB breakthrough infection exhibited robust neutralizing activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection. Although BA.2.86 showed greater resistance to mAbs to subdomain 1 (SD1) and receptor-binding domain (RBD) class 2 and 3 epitopes, it was more sensitive to mAbs to class 1 and 4/1 epitopes in the 'inner face' of the RBD that is exposed only when this domain is in the 'up' position. We also identified six new spike mutations that mediate antibody resistance, including E554K that threatens SD1 mAbs in clinical development. The BA.2.86 spike also had a remarkably high receptor affinity. The ultimate trajectory of this new SARS-CoV-2 variant will soon be revealed by continuing surveillance, but its worldwide spread is worrisome.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Liyuan Liu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Logan T Schwanz
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathobiology and Mechanisms of Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jerren Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Richard M Zhang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yiming Qu
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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7
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McCool RS, Musayev M, Bush SM, Derrien-Colemyn A, Acreman CM, Wrapp D, Ruckwardt TJ, Graham BS, Mascola JR, McLellan JS. Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein elicits antibodies targeting a membrane-proximal epitope. J Virol 2023; 97:e0092923. [PMID: 37737588 PMCID: PMC10617438 DOI: 10.1128/jvi.00929-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and pneumonia in infants, infecting all children by age 5. RSV also causes substantial morbidity and mortality in older adults, and a vaccine for older adults based on a prefusion-stabilized form of the viral F glycoprotein was recently approved by the FDA. Here, we investigate a set of antibodies that belong to the same public clonotype and were isolated from individuals vaccinated with a prefusion-stabilized RSV F protein. Our results reveal that these antibodies are highly potent and recognize a previously uncharacterized antigenic site on the prefusion F protein. Vaccination with prefusion RSV F proteins appears to boost the elicitation of these neutralizing antibodies, which are not commonly elicited by natural infection.
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Affiliation(s)
- Ryan S. McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Maryam Musayev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina M. Bush
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexandrine Derrien-Colemyn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cory M. Acreman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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8
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Rao PG, Lambert GS, Upadhyay C. Broadly neutralizing antibody epitopes on HIV-1 particles are exposed after virus interaction with host cells. J Virol 2023; 97:e0071023. [PMID: 37681958 PMCID: PMC10537810 DOI: 10.1128/jvi.00710-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/07/2023] [Indexed: 09/09/2023] Open
Abstract
The envelope (Env) glycoproteins on HIV-1 virions are the sole target of broadly neutralizing antibodies (bNAbs) and the focus of vaccines. However, many cross-reactive conserved epitopes are often occluded on virus particles, contributing to the evasion of humoral immunity. This study aimed to identify the Env epitopes that are exposed/occluded on HIV-1 particles and to investigate the mechanisms contributing to their masking. Using a flow cytometry-based assay, three HIV-1 isolates, and a panel of antibodies, we show that only select epitopes, including V2i, the gp120-g41 interface, and gp41-MPER, are accessible on HIV-1 particles, while V3, V2q, and select CD4bs epitopes are masked. These epitopes become accessible after allosteric conformational changes are induced by the pre-binding of select Abs, prompting us to test if similar conformational changes are required for these Abs to exhibit their neutralization capability. We tested HIV-1 neutralization where the virus-mAb mix was pre-incubated/not pre-incubated for 1 hour prior to adding the target cells. Similar levels of neutralization were observed under both assay conditions, suggesting that the interaction between virus and target cells sensitizes the virions for neutralization via bNAbs. We further show that lectin-glycan interactions can also expose these epitopes. However, this effect is dependent on the lectin specificity. Given that, bNAbs are ideal for providing sterilizing immunity and are the goal of current HIV-1 vaccine efforts, these data offer insight on how HIV-1 may occlude these vulnerable epitopes from the host immune response. In addition, the findings can guide the formulation of effective antibody combinations for therapeutic use. IMPORTANCE The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein mediates viral entry and is the sole target of neutralizing antibodies. Our data suggest that antibody epitopes including V2q (e.g., PG9, PGT145), CD4bs (e.g., VRC01, 3BNC117), and V3 (2219, 2557) are masked on HIV-1 particles. The PG9 and 2219 epitopes became accessible for binding after conformational unmasking was induced by the pre-binding of select mAbs. Attempts to understand the masking mechanism led to the revelation that interaction between virus and host cells is needed to sensitize the virions for neutralization by broadly neutralizing antibodies (bNAbs). These data provide insight on how bNAbs may gain access to these occluded epitopes to exert their neutralization effects and block HIV-1 infection. These findings have important implications for the way we evaluate the neutralizing efficacy of antibodies and can potentially guide vaccine design.
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Affiliation(s)
- Priyanka Gadam Rao
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gregory S. Lambert
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chitra Upadhyay
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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9
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Ezzemani W, Windisch MP, Altawalah H, Guessous F, Saile R, Benjelloun S, Kettani A, Ezzikouri S. Design of a multi-epitope Zika virus vaccine candidate - an in-silico study. J Biomol Struct Dyn 2023; 41:3762-3771. [PMID: 35318896 DOI: 10.1080/07391102.2022.2055648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/15/2022] [Indexed: 01/12/2023]
Abstract
Zika virus (ZIKV), an RNA virus, rapidly spreads Aedes mosquito-borne sickness. Currently, there are neither effective vaccines nor therapeutics available to prevent or treat ZIKV infection. In this study, to address these unmet medical needs, we aimed to design B- and T-cell candidate multi-epitope-based subunit against ZIKV using an in silico approach. In this study we applied immunoinformatics, molecular docking, and dynamic simulation assessments targeting the most immunogenic proteins; the capsid (C), envelope (E) proteins and the non-stuctural protein (NS1), described in our previous study, and which predicted immunodominant B and T cell epitopes. The final non-allergenic and highly antigenic multi-epitope was constituted of immunogenic screened-epitopes (3 CTL and 3 HTL) and the β-defensin as an adjuvant that have been linked using EAAAK, AAY, and GPGPG linkers, respectively. The final construct containing 143 amino acids was characterized for its allergenicity, antigenicity, and physiochemical properties; and found to be safe and immunogenic with a good prediction of solubility. The existence of IFN-γ epitopes asserts the capacity to trigger strong immune responses. Subsequently, the molecular docking among vaccine and immune receptors (TLR2/TLR4) was revealed with a good binding affinity with and stable molecular interactions. Molecular dynamics simulation confirmed the stability of the complexes. Finally, the construct was subjected to in silico cloning demonstrating the efficiently of its expression in E.coli. However, this study needs the experimental validation to demonstrate vaccine safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Marc P Windisch
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
- Virology Unit, Yacoub Behbehani center, Sabah Hospital, Ministry of Health, Kuwait
| | - Fadila Guessous
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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10
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Alsoussi WB, Malladi SK, Zhou JQ, Liu Z, Ying B, Kim W, Schmitz AJ, Lei T, Horvath SC, Sturtz AJ, McIntire KM, Evavold B, Han F, Scheaffer SM, Fox IF, Mirza SF, Parra-Rodriguez L, Nachbagauer R, Nestorova B, Chalkias S, Farnsworth CW, Klebert MK, Pusic I, Strnad BS, Middleton WD, Teefey SA, Whelan SPJ, Diamond MS, Paris R, O'Halloran JA, Presti RM, Turner JS, Ellebedy AH. SARS-CoV-2 Omicron boosting induces de novo B cell response in humans. Nature 2023; 617:592-598. [PMID: 37011668 DOI: 10.1038/s41586-023-06025-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
The primary two-dose SARS-CoV-2 mRNA vaccine series are strongly immunogenic in humans, but the emergence of highly infectious variants necessitated additional doses and the development of vaccines aimed at the new variants1-4. SARS-CoV-2 booster immunizations in humans primarily recruit pre-existing memory B cells5-9. However, it remains unclear whether the additional doses induce germinal centre reactions whereby re-engaged B cells can further mature, and whether variant-derived vaccines can elicit responses to variant-specific epitopes. Here we show that boosting with an mRNA vaccine against the original monovalent SARS-CoV-2 mRNA vaccine or the bivalent B.1.351 and B.1.617.2 (Beta/Delta) mRNA vaccine induced robust spike-specific germinal centre B cell responses in humans. The germinal centre response persisted for at least eight weeks, leading to significantly more mutated antigen-specific bone marrow plasma cell and memory B cell compartments. Spike-binding monoclonal antibodies derived from memory B cells isolated from individuals boosted with either the original SARS-CoV-2 spike protein, bivalent Beta/Delta vaccine or a monovalent Omicron BA.1-based vaccine predominantly recognized the original SARS-CoV-2 spike protein. Nonetheless, using a more targeted sorting approach, we isolated monoclonal antibodies that recognized the BA.1 spike protein but not the original SARS-CoV-2 spike protein from individuals who received the mRNA-1273.529 booster; these antibodies were less mutated and recognized novel epitopes within the spike protein, suggesting that they originated from naive B cells. Thus, SARS-CoV-2 booster immunizations in humans induce robust germinal centre B cell responses and can generate de novo B cell responses targeting variant-specific epitopes.
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Affiliation(s)
- Wafaa B Alsoussi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Sameer Kumar Malladi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Baoling Ying
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Stephen C Horvath
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Alexandria J Sturtz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Katherine M McIntire
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Birk Evavold
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Fangjie Han
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Suzanne M Scheaffer
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Isabella F Fox
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Senaa F Mirza
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Luis Parra-Rodriguez
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Christopher W Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael K Klebert
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Iskra Pusic
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin S Strnad
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | | | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
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11
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Schaefer-Babajew D, Wang Z, Muecksch F, Cho A, Loewe M, Cipolla M, Raspe R, Johnson B, Canis M, DaSilva J, Ramos V, Turroja M, Millard KG, Schmidt F, Witte L, Dizon J, Shimeliovich I, Yao KH, Oliveira TY, Gazumyan A, Gaebler C, Bieniasz PD, Hatziioannou T, Caskey M, Nussenzweig MC. Antibody feedback regulates immune memory after SARS-CoV-2 mRNA vaccination. Nature 2023; 613:735-742. [PMID: 36473496 PMCID: PMC9876794 DOI: 10.1038/s41586-022-05609-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Feedback inhibition of humoral immunity by antibodies was first documented in 19091. Subsequent studies showed that, depending on the context, antibodies can enhance or inhibit immune responses2,3. However, little is known about how pre-existing antibodies influence the development of memory B cells. Here we examined the memory B cell response in individuals who received two high-affinity anti-SARS-CoV-2 monoclonal antibodies and subsequently two doses of an mRNA vaccine4-8. We found that the recipients of the monoclonal antibodies produced antigen-binding and neutralizing titres that were only fractionally lower compared than in control individuals. However, the memory B cells of the individuals who received the monoclonal antibodies differed from those of control individuals in that they predominantly expressed low-affinity IgM antibodies that carried small numbers of somatic mutations and showed altered receptor binding domain (RBD) target specificity, consistent with epitope masking. Moreover, only 1 out of 77 anti-RBD memory antibodies tested neutralized the virus. The mechanism underlying these findings was examined in experiments in mice that showed that germinal centres formed in the presence of the same antibodies were dominated by low-affinity B cells. Our results indicate that pre-existing high-affinity antibodies bias germinal centre and memory B cell selection through two distinct mechanisms: (1) by lowering the activation threshold for B cells, thereby permitting abundant lower-affinity clones to participate in the immune response; and (2) through direct masking of their cognate epitopes. This may in part explain the shifting target profile of memory antibodies elicited by booster vaccinations9.
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Affiliation(s)
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Maximilian Loewe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Brianna Johnson
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Leander Witte
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | | | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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12
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Lee JH, Sutton HJ, Cottrell CA, Phung I, Ozorowski G, Sewall LM, Nedellec R, Nakao C, Silva M, Richey ST, Torres JL, Lee WH, Georgeson E, Kubitz M, Hodges S, Mullen TM, Adachi Y, Cirelli KM, Kaur A, Allers C, Fahlberg M, Grasperge BF, Dufour JP, Schiro F, Aye PP, Kalyuzhniy O, Liguori A, Carnathan DG, Silvestri G, Shen X, Montefiori DC, Veazey RS, Ward AB, Hangartner L, Burton DR, Irvine DJ, Schief WR, Crotty S. Long-primed germinal centres with enduring affinity maturation and clonal migration. Nature 2022; 609:998-1004. [PMID: 36131022 PMCID: PMC9491273 DOI: 10.1038/s41586-022-05216-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/09/2022] [Indexed: 02/06/2023]
Abstract
Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (BGC) cells that last for at least 6 months. A 186-fold increase in BGC cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells1,2. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivy Phung
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Murillo Silva
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sam Hodges
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tina-Marie Mullen
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kimberly M Cirelli
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Carolina Allers
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Marissa Fahlberg
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Brooke F Grasperge
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Jason P Dufour
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Faith Schiro
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Pyone P Aye
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Oleksandr Kalyuzhniy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Diane G Carnathan
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Guido Silvestri
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiaoying Shen
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - David C Montefiori
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lars Hangartner
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Darrell J Irvine
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
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13
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Cao Y, Yisimayi A, Jian F, Song W, Xiao T, Wang L, Du S, Wang J, Li Q, Chen X, Yu Y, Wang P, Zhang Z, Liu P, An R, Hao X, Wang Y, Wang J, Feng R, Sun H, Zhao L, Zhang W, Zhao D, Zheng J, Yu L, Li C, Zhang N, Wang R, Niu X, Yang S, Song X, Chai Y, Hu Y, Shi Y, Zheng L, Li Z, Gu Q, Shao F, Huang W, Jin R, Shen Z, Wang Y, Wang X, Xiao J, Xie XS. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 2022; 608:593-602. [PMID: 35714668 DOI: 10.21203/rs.3.rs-1611421/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/15/2022] [Indexed: 05/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility than the BA.2 lineage1. The receptor binding and immune-evasion capability of these recently emerged variants require immediate investigation. Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar binding affinities to BA.2 for the angiotensin-converting enzyme 2 (ACE2) receptor. Of note, BA.2.12.1 and BA.4/BA.5 display increased evasion of neutralizing antibodies compared with BA.2 against plasma from triple-vaccinated individuals or from individuals who developed a BA.1 infection after vaccination. To delineate the underlying antibody-evasion mechanism, we determined the escape mutation profiles2, epitope distribution3 and Omicron-neutralization efficiency of 1,640 neutralizing antibodies directed against the receptor-binding domain of the viral spike protein, including 614 antibodies isolated from people who had recovered from BA.1 infection. BA.1 infection after vaccination predominantly recalls humoral immune memory directed against ancestral (hereafter referred to as wild-type (WT)) SARS-CoV-2 spike protein. The resulting elicited antibodies could neutralize both WT SARS-CoV-2 and BA.1 and are enriched on epitopes on spike that do not bind ACE2. However, most of these cross-reactive neutralizing antibodies are evaded by spike mutants L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1. Nevertheless, these neutralizing antibodies are largely evaded by BA.2 and BA.4/BA.5 owing to D405N and F486V mutations, and react weakly to pre-Omicron variants, exhibiting narrow neutralization breadths. The therapeutic neutralizing antibodies bebtelovimab4 and cilgavimab5 can effectively neutralize BA.2.12.1 and BA.4/BA.5, whereas the S371F, D405N and R408S mutations undermine most broadly sarbecovirus-neutralizing antibodies. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antigenic Drift and Shift/genetics
- Antigenic Drift and Shift/immunology
- COVID-19/immunology
- COVID-19/transmission
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Humans
- Immune Tolerance
- Immunity, Humoral
- Immunization, Secondary
- Mutation
- Neutralization Tests
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Weiliang Song
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Tianhe Xiao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
| | - Lei Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuo Du
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Jing Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
| | - Xiaosu Chen
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Yuanling Yu
- Changping Laboratory, Beijing, P. R. China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
| | - Peng Wang
- Changping Laboratory, Beijing, P. R. China
| | - Zhiying Zhang
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Pulan Liu
- School of Life Sciences, Peking University, Beijing, P. R. China
| | - Ran An
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
| | - Xiaohua Hao
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Yao Wang
- Changping Laboratory, Beijing, P. R. China
| | - Jing Wang
- Changping Laboratory, Beijing, P. R. China
| | - Rui Feng
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Haiyan Sun
- Changping Laboratory, Beijing, P. R. China
| | | | - Wen Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Dong Zhao
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | | | | | - Can Li
- Changping Laboratory, Beijing, P. R. China
| | - Na Zhang
- Changping Laboratory, Beijing, P. R. China
| | - Rui Wang
- Changping Laboratory, Beijing, P. R. China
| | - Xiao Niu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Sijie Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P. R. China
| | | | - Yangyang Chai
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Ye Hu
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | - Yansong Shi
- Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China
| | | | - Zhiqiang Li
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
| | | | - Fei Shao
- Changping Laboratory, Beijing, P. R. China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, P. R. China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China.
| | - Youchun Wang
- Changping Laboratory, Beijing, P. R. China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, P. R. China.
| | - Xiangxi Wang
- Changping Laboratory, Beijing, P. R. China.
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.
| | - Junyu Xiao
- Changping Laboratory, Beijing, P. R. China.
- School of Life Sciences, Peking University, Beijing, P. R. China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China.
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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14
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Tajuelo A, López-Siles M, Más V, Pérez-Romero P, Aguado JM, Briz V, McConnell MJ, Martín-Galiano AJ, López D. Cross-Recognition of SARS-CoV-2 B-Cell Epitopes with Other Betacoronavirus Nucleoproteins. Int J Mol Sci 2022; 23:ijms23062977. [PMID: 35328398 PMCID: PMC8955325 DOI: 10.3390/ijms23062977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.
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Affiliation(s)
- Ana Tajuelo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Mireia López-Siles
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Pilar Pérez-Romero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | | | - Verónica Briz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Michael J. McConnell
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
| | - Antonio J. Martín-Galiano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
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15
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Cameroni E, Bowen JE, Rosen LE, Saliba C, Zepeda SK, Culap K, Pinto D, VanBlargan LA, De Marco A, di Iulio J, Zatta F, Kaiser H, Noack J, Farhat N, Czudnochowski N, Havenar-Daughton C, Sprouse KR, Dillen JR, Powell AE, Chen A, Maher C, Yin L, Sun D, Soriaga L, Bassi J, Silacci-Fregni C, Gustafsson C, Franko NM, Logue J, Iqbal NT, Mazzitelli I, Geffner J, Grifantini R, Chu H, Gori A, Riva A, Giannini O, Ceschi A, Ferrari P, Cippà PE, Franzetti-Pellanda A, Garzoni C, Halfmann PJ, Kawaoka Y, Hebner C, Purcell LA, Piccoli L, Pizzuto MS, Walls AC, Diamond MS, Telenti A, Virgin HW, Lanzavecchia A, Snell G, Veesler D, Corti D. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature 2022. [PMID: 35016195 DOI: 10.1101/2021.12.12.472269v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody-based therapeutics. Here we show that the Omicron RBD binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1 RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity were observed against Omicron compared to the ancestral pseudovirus in plasma from convalescent individuals and from individuals who had been vaccinated against SARS-CoV-2, but this loss was less pronounced after a third dose of vaccine. Most monoclonal antibodies that are directed against the receptor-binding motif lost in vitro neutralizing activity against Omicron, with only 3 out of 29 monoclonal antibodies retaining unaltered potency, including the ACE2-mimicking S2K146 antibody1. Furthermore, a fraction of broadly neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through recognition of antigenic sites outside the receptor-binding motif, including sotrovimab2, S2X2593 and S2H974. The magnitude of Omicron-mediated immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly neutralizing monoclonal antibodies that recognize RBD epitopes that are conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigenic Drift and Shift/genetics
- Antigenic Drift and Shift/immunology
- Broadly Neutralizing Antibodies/immunology
- COVID-19 Vaccines/immunology
- Cell Line
- Convalescence
- Epitopes, B-Lymphocyte/immunology
- Humans
- Immune Evasion
- Mice
- Neutralization Tests
- SARS-CoV-2/chemistry
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vesiculovirus/genetics
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Affiliation(s)
- Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Laura A VanBlargan
- Department of Medicine, Washington University of School of Medicine, St Louis, MO, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Li Yin
- Vir Biotechnology, San Francisco, CA, USA
| | - David Sun
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Nicholas M Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Ignacio Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Andrea Gori
- Infectious Disease Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences 'L.Sacco' (DIBIC), Università di Milano, Milan, Italy
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Pietro E Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University of School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
- National Institute of Molecular Genetics, Milan, Italy
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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16
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Vengesai A, Kasambala M, Mutandadzi H, Mduluza-Jokonya TL, Mduluza T, Naicker T. Scoping review of the applications of peptide microarrays on the fight against human infections. PLoS One 2022; 17:e0248666. [PMID: 35077448 PMCID: PMC8789108 DOI: 10.1371/journal.pone.0248666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 01/11/2022] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION This scoping review explores the use of peptide microarrays in the fight against infectious diseases. The research domains explored included the use of peptide microarrays in the mapping of linear B-cell and T cell epitopes, antimicrobial peptide discovery, immunosignature characterisation and disease immunodiagnostics. This review also provides a short overview of peptide microarray synthesis. METHODS Electronic databases were systematically searched to identify relevant studies. The review was conducted using the Joanna Briggs Institute methodology for scoping reviews and data charting was performed using a predefined form. The results were reported by narrative synthesis in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews guidelines. RESULTS Ninety-five articles from 103 studies were included in the final data charting process. The majority (92. 0%) of the articles were published during 2010-2020 and were mostly from Europe (44.2%) and North America (34.7%). The findings were from the investigation of viral (45.6%), bacterial (32. 0%), parasitic (23.3%) and fungal (2. 0%) infections. Out of the serological studies, IgG was the most reported antibody type followed by IgM. The largest portion of the studies (77.7%) were related to mapping B-cell linear epitopes, 5.8% were on diagnostics, 5.8% reported on immunosignature characterisation and 8.7% reported on viral and bacterial cell binding assays. Two studies reported on T-cell epitope profiling. CONCLUSION The most important application of peptide microarrays was found to be B-cell epitope mapping or antibody profiling to identify diagnostic and vaccine targets. Immunosignatures identified by random peptide microarrays were found to be applied in the diagnosis of infections and interrogation of vaccine responses. The analysis of the interactions of random peptide microarrays with bacterial and viral cells using binding assays enabled the identification of antimicrobial peptides. Peptide microarray arrays were also used for T-cell linear epitope mapping which may provide more information for the design of peptide-based vaccines and for the development of diagnostic reagents.
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Affiliation(s)
- Arthur Vengesai
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
| | - Maritha Kasambala
- Department of Biology, Faculty of Science and Agriculture, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Hamlet Mutandadzi
- Faculty of Medicine and Health Sciences, Parirenyatwa Hospital, University of Zimbabwe, Harare, Zimbabwe
| | - Tariro L. Mduluza-Jokonya
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Takafira Mduluza
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
| | - Thajasvarie Naicker
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
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Polyiam K, Ruengjitchatchawalya M, Mekvichitsaeng P, Kaeoket K, Hoonsuwan T, Joiphaeng P, Roshorm YM. Immunodominant and Neutralizing Linear B-Cell Epitopes Spanning the Spike and Membrane Proteins of Porcine Epidemic Diarrhea Virus. Front Immunol 2022; 12:785293. [PMID: 35126354 PMCID: PMC8807655 DOI: 10.3389/fimmu.2021.785293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is the causative agent of PED, an enteric disease that causes high mortality rates in piglets. PEDV is an alphacoronavirus that has high genetic diversity. Insights into neutralizing B-cell epitopes of all genetically diverse PEDV strains are of importance, particularly for designing a vaccine that can provide broad protection against PEDV. In this work, we aimed to explore the landscape of linear B-cell epitopes on the spike (S) and membrane (M) proteins of global PEDV strains. All amino acid sequences of the PEDV S and M proteins were retrieved from the NCBI database and grouped. Immunoinformatics-based methods were next developed and used to identify putative linear B-cell epitopes from 14 and 5 consensus sequences generated from distinct groups of the S and M proteins, respectively. ELISA testing predicted peptides with PEDV-positive sera revealed nine novel immunodominant epitopes on the S protein. Importantly, seven of these novel immunodominant epitopes and other subdominant epitopes were demonstrated to be neutralizing epitopes by neutralization–inhibition assay. Our findings unveil important roles of the PEDV S2 subunit in both immune stimulation and virus neutralization. Additionally, our study shows the first time that the M protein is also the target of PEDV neutralization with seven neutralizing epitopes identified. Conservancy profiles of the epitopes are also provided. In this study, we offer immunoinformatics-based methods for linear B-cell epitope identification and a more complete profile of linear B-cell epitopes across the PEDV S and M proteins, which may contribute to the development of a greater next-generation PEDV vaccine as well as peptide-based immunoassays.
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Affiliation(s)
- Kanokporn Polyiam
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Marasri Ruengjitchatchawalya
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Sciences, Mahidol University, Salaya, Thailand
| | | | | | - Yaowaluck Maprang Roshorm
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- *Correspondence: Yaowaluck Maprang Roshorm,
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18
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Brown JW, Das KK, Kalas V, Das KM, Mills JC. mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PLoS One 2021; 16:e0261082. [PMID: 34910746 PMCID: PMC8673611 DOI: 10.1371/journal.pone.0261082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Multiple previous studies have shown the monoclonal antibody Das-1 (formerly called 7E12H12) is specifically reactive towards metaplastic and carcinomatous lesions in multiple organs of the gastrointestinal system (e.g. Barrett's esophagus, intestinal-type metaplasia of the stomach, gastric adenocarcinoma, high-grade pancreatic intraepithelial neoplasm, and pancreatic ductal adenocarcinoma) as well as in other organs (bladder and lung carcinomas). Beyond being a useful biomarker in tissue, mAb Das-1 has recently proven to be more accurate than current paradigms for identifying cysts harboring advanced neoplasia. Though this antibody has been used extensively for clinical, basic science, and translational applications for decades, its epitope has remained elusive. METHODS In this study, we chemically deglycosylated a standard source of antigen, which resulted in near complete loss of the signal as measured by western blot analysis. The epitope recognized by mAb Das-1 was determined by affinity to a comprehensive glycan array and validated by inhibition of a direct ELISA. RESULTS The epitope recognized by mAb Das-1 is 3'-Sulfo-Lewis A/C (3'-Sulfo-LeA/C). 3'-Sulfo-LeA/C is broadly reexpressed across numerous GI epithelia and elsewhere during metaplastic and carcinomatous transformation. DISCUSSION 3'-Sulfo-LeA/C is a clinically important antigen that can be detected both intracellularly in tissue using immunohistochemistry and extracellularly in cyst fluid and serum by ELISA. The results open new avenues for tumorigenic risk stratification of various gastrointestinal lesions.
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Affiliation(s)
- Jeffrey W. Brown
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
| | - Koushik K. Das
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
| | - Vasilios Kalas
- Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
- Physician Scientist Training Program, Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, Illinois, United States of America
| | - Kiron M. Das
- Division of Gastroenterology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Jason C. Mills
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
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Cho A, Muecksch F, Schaefer-Babajew D, Wang Z, Finkin S, Gaebler C, Ramos V, Cipolla M, Mendoza P, Agudelo M, Bednarski E, DaSilva J, Shimeliovich I, Dizon J, Daga M, Millard KG, Turroja M, Schmidt F, Zhang F, Tanfous TB, Jankovic M, Oliveria TY, Gazumyan A, Caskey M, Bieniasz PD, Hatziioannou T, Nussenzweig MC. Anti-SARS-CoV-2 receptor-binding domain antibody evolution after mRNA vaccination. Nature 2021; 600:517-522. [PMID: 34619745 PMCID: PMC8674133 DOI: 10.1038/s41586-021-04060-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces B cell responses that continue to evolve for at least a year. During that time, memory B cells express increasingly broad and potent antibodies that are resistant to mutations found in variants of concern1. As a result, vaccination of coronavirus disease 2019 (COVID-19) convalescent individuals with currently available mRNA vaccines produces high levels of plasma neutralizing activity against all variants tested1,2. Here we examine memory B cell evolution five months after vaccination with either Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) mRNA vaccine in a cohort of SARS-CoV-2-naive individuals. Between prime and boost, memory B cells produce antibodies that evolve increased neutralizing activity, but there is no further increase in potency or breadth thereafter. Instead, memory B cells that emerge five months after vaccination of naive individuals express antibodies that are similar to those that dominate the initial response. While individual memory antibodies selected over time by natural infection have greater potency and breadth than antibodies elicited by vaccination, the overall neutralizing potency of plasma is greater following vaccination. These results suggest that boosting vaccinated individuals with currently available mRNA vaccines will increase plasma neutralizing activity but may not produce antibodies with equivalent breadth to those obtained by vaccinating convalescent individuals.
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Affiliation(s)
- Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Mridushi Daga
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Tarek Ben Tanfous
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thiago Y Oliveria
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | | | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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20
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Abdollahi S, Raoufi Z, Fakoor MH. Physicochemical and structural characterization, epitope mapping and vaccine potential investigation of a new protein containing Tetratrico Peptide Repeats of Acinetobacter baumannii: An in-silico and in-vivo approach. Mol Immunol 2021; 140:22-34. [PMID: 34649027 DOI: 10.1016/j.molimm.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
Abstract
Acinetobacter baumannii is an opportunistic multidrug-resistant pathogen that causes a significant mortality rate. The proteins containing Tetratrico Peptide Repeats (TPRs) are involved in the pathogenicity and virulence of bacteria and have different roles such as transfer of bacterial virulence factors to host cells, binding to the host cells and inhibition of phagolysosomal maturation. So, in this study, physicochemical properties of a new protein containing TPRs in A. baumannii which was named PcTPRs1 by this study were characterized and its 3D structure was predicted by in-silico tools. The protein B and T cell epitopes were mapped and its vaccine potential was in-silico and in-vivo investigated. Domain analysis indicated that the protein contains the Flp pilus assembly protein TadD domain which has three TPRs. The helix is dominant in the protein structure, and this protein is an outer membrane antigen which, is extremely conserved among A. baumannii strains; thus, has good properties to be applied as a recombinant vaccine. The best-predicted and refined model was applied in ligand-binding sites and conformational epitopes prediction. Based on epitope mapping results, several epitopes were characterized which could stimulate both immune systems. BLAST results showed the introduced epitopes are completely conserved among A. baumannii strains. The in-vivo analysis indicates that a 101 amino acid fragment of the protein which contains the best selected epitope, can produce a good protectivity against A. baumannii as well as the whole TPR protein and thus could be investigated as an effective subunit and potential vaccines.
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Affiliation(s)
- Sajad Abdollahi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
| | - Zeinab Raoufi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
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21
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Jalal K, Khan K, Ahmad D, Hayat A, Basharat Z, Abbas MN, Alghamdi S, Almehmadi M, Sahibzada MUK. Pan-Genome Reverse Vaccinology Approach for the Design of Multi-Epitope Vaccine Construct against Escherichia albertii. Int J Mol Sci 2021; 22:12814. [PMID: 34884620 PMCID: PMC8657462 DOI: 10.3390/ijms222312814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/21/2022] Open
Abstract
Escherichia albertii is characterized as an emerging pathogen, causing enteric infections. It is responsible for high mortality rate, especially in children, elderly, and immunocompromised people. To the best of our knowledge, no vaccine exists to curb this pathogen. Therefore, in current study, we aimed to identify potential vaccine candidates and design chimeric vaccine models against Escherichia albertii from the analysis of publicly available data of 95 strains, using a reverse vaccinology approach. Outer-membrane proteins (n = 4) were identified from core genome as vaccine candidates. Eventually, outer membrane Fimbrial usher (FimD) protein was selected as a promiscuous vaccine candidate and utilized to construct a potential vaccine model. It resulted in three epitopes, leading to the design of twelve vaccine constructs. Amongst these, V6 construct was found to be highly immunogenic, non-toxic, non-allergenic, antigenic, and most stable. This was utilized for molecular docking and simulation studies against six HLA and two TLR complexes. This construct can therefore be used for pan-therapy against different strains of E. albertii and needs to be tested in vitro and in vivo.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Science, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi 75270, Pakistan; (K.J.); (D.A.)
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi 75270, Pakistan;
| | - Diyar Ahmad
- International Center for Chemical and Biological Science, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi 75270, Pakistan; (K.J.); (D.A.)
| | - Ajmal Hayat
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan;
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Muhammad Naseer Abbas
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan;
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia;
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22
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Soltan MA, Eldeen MA, Elbassiouny N, Kamel HL, Abdelraheem KM, El-Gayyed HA, Gouda AM, Sheha MF, Fayad E, Ali OAA, Ghany KAE, El-damasy DA, Darwish KM, Elhady SS, Sileem AE. In Silico Designing of a Multitope Vaccine against Rhizopus microsporus with Potential Activity against Other Mucormycosis Causing Fungi. Cells 2021; 10:3014. [PMID: 34831237 PMCID: PMC8616407 DOI: 10.3390/cells10113014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Nada Elbassiouny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Hasnaa L. Kamel
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Kareem M. Abdelraheem
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Hanaa Abd El-Gayyed
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Ahmed M. Gouda
- Department of Pharmacy Practice, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt;
| | - Mohammed F. Sheha
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | | | - Dalia A. El-damasy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Ashraf E. Sileem
- Department of Chest Diseases, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
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23
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Zhang W, Wang W, Liu X, Chen Y, Ouyang K, Wei Z, Liu H, Huang W. Identification of novel B-cell epitopes on the capsid protein of type 1 porcine astrovirus, using monoclonal antibodies. Int J Biol Macromol 2021; 189:939-947. [PMID: 34464644 DOI: 10.1016/j.ijbiomac.2021.08.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Porcine astrovirus (PAstV) is prevalent in pigs worldwide and could cause clinical symptoms such as diarrhea and encephalitis. The capsid protein (Cap) of PAstV plays a determinant role for virus immunological characteristics. In this study, the major antigenic regions of PAstV1 Cap were expressed through prokaryotic expression systems and immunized to BALB/c mice. Finally, two anti-Cap monoclonal antibodies (named mAb F4-4 and D3F10) were screened by indirect immune-fluorescence assay (IFA). A series of truncated GST-fused or artificially synthesized peptides were used to detect their reactivity with the mAbs and PAstV positive serum. Two novel B cell epitopes (120-GNNTFG-125, 485-RISDPTWFSA-494) were identified by using these two mAbs. Moreover, sequence alignment result showed that epitope 120-GNNTFG-125 was highly conserved in type 1 PAstV capsid protein. Cross-reactivity analysis further confirmed the genotype-specificity of mAb F4-4. The results of this study demonstrated to be the first description of monoclonal antibody preparation and B-cell epitope mapping on PAstV capsid protein, which may provide new information on the biological significance of PAstV capsid protein and lay a foundation for the development of PAstV immunological tests and genotype diagnostic methods.
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Affiliation(s)
- Wenchao Zhang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Weiyi Wang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Xin Liu
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Ying Chen
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Kang Ouyang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Zuzhang Wei
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China
| | - Huan Liu
- Department of Scientific Research, The First Affiliated Hospital of Guangxi University of Chinese Medicine, No. 89-9 Dongge Road, Nanning 530024, China.
| | - Weijian Huang
- College of Animal Science and Technology, Guangxi University, No. 100 Daxue Road, Nanning 530005, China.
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Sharma S, Vashisht S, Gaur SN, Lavasa S, Arora N. Identification of B cell epitopes of Per a 5 allergen using bioinformatic approach. Immunobiology 2021; 226:152146. [PMID: 34717182 DOI: 10.1016/j.imbio.2021.152146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/10/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Immune epitopes of allergens are pivotal for development of novel diagnostic and therapeutic modalities. Present study aims to identify antigenic determinants of Per a 5, a clinically relevant cross reactive cockroach allergen. METHODS The three dimensional structure of Per a 5 was modelled using Modeller 9v11 software. A combination of sequence and structure based computational tools were employed for predicting B cell epitopes. Epitopes were synthesized and immunoreactivity was assessed by ELISA using cockroach hypersensitive patient's sera. Cross-reactivity potential of predicted epitopes was assessed with SDAP and ConSurf and validated by IgE ELISA with fungal and mite hypersensitive patient's sera. RESULTS Per a 5 structure exhibited good quality factor in ERRAT and high stereochemical stability. In silico analysis revealed six B cell epitopes (BC-P1 to P6). BC-P3 demonstrated significant IgE binding followed by BC-P2 and BC-P1 with cockroach hypersensitive patient's sera. Per a 5 epitopes demonstrate considerable similarity with broad spectrum of allergens from fungal, mites, helminths, fruits and nuts. Analysis of PD values indicate BC-P4 to be well conserved among dust mite and helminth GSTs (8.89, 10.63 and 10.69 with D. pteronyssinus, W. bancrofti and F. hepatica respectively). ConSurf analysis of Per a 5 revealed specific enrichment of evolutionarily similar amino acid residues in BC-P2 (with fungal and mite GSTs) and BC-P4 (with mite and helminth GSTs). Further, IgE binding analysis of epitopes demonstrate BC-P2, BC-P3 and BC-P5 as high IgE binders in fungal hypersensitive sera while BC-P1, BC-P2, BC-P4 and BC-P5 demonstrated significant IgE binding with mite hypersensitive sera. CONCLUSIONS Among the predicted epitopes, BC-P3 demonstrates maximal IgE binding ability. Computational analysis suggests strong evolutionary conservation and cross reactive potential of BC-P4 with allergens in dust mite and helminths. ELISA highlights predictive potential of analysing evolutionarily conserved residues for uncovering potentially cross reactive antigenic determinants. GENERAL SIGNIFICANCE Immune epitopes of Per a 5 were identified for aiding molecular diagnosis and potential cross reactivity.
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Affiliation(s)
- Swati Sharma
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110007, India; Academy of Scientific and Innovative Research, Ghaziabad, U.P., 201002, India
| | - Srishti Vashisht
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110007, India
| | - S N Gaur
- Department of Pulmonary Medicine, V.P. Chest Institute, University of Delhi, New Delhi 110007, India
| | | | - Naveen Arora
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110007, India; Academy of Scientific and Innovative Research, Ghaziabad, U.P., 201002, India
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25
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Errico JM, Zhao H, Chen RE, Liu Z, Case JB, Ma M, Schmitz AJ, Rau MJ, Fitzpatrick JAJ, Shi PY, Diamond MS, Whelan SPJ, Ellebedy AH, Fremont DH. Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep 2021; 37:109881. [PMID: 34655519 PMCID: PMC8498651 DOI: 10.1016/j.celrep.2021.109881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/11/2021] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has necessitated the rapid development of antibody-based therapies and vaccines as countermeasures. Here, we use cryoelectron microscopy (cryo-EM) to characterize two protective anti-SARS-CoV-2 murine monoclonal antibodies (mAbs) in complex with the spike protein, revealing similarities between epitopes targeted by human and murine B cells. The more neutralizing mAb, 2B04, binds the receptor-binding motif (RBM) of the receptor-binding domain (RBD) and competes with angiotensin-converting enzyme 2 (ACE2). By contrast, 2H04 binds adjacent to the RBM and does not compete for ACE2 binding. Naturally occurring sequence variants of SARS-CoV-2 and corresponding neutralization escape variants selected in vitro map to our structurally defined epitopes, suggesting that SARS-CoV-2 might evade therapeutic antibodies with a limited set of mutations, underscoring the importance of combination mAb therapeutics. Finally, we show that 2B04 neutralizes SARS-CoV-2 infection by preventing ACE2 engagement, whereas 2H04 reduces host cell attachment without directly disrupting ACE2-RBM interactions, providing distinct inhibitory mechanisms used by RBD-specific mAbs.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- COVID-19/immunology
- Cryoelectron Microscopy
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Humans
- Mice
- Protein Interaction Domains and Motifs/immunology
- Protein Structure, Quaternary
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Haiyan Zhao
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Meisheng Ma
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA; Departments of Neuroscience and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ali H Ellebedy
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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26
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Polyiam K, Phoolcharoen W, Butkhot N, Srisaowakarn C, Thitithanyanont A, Auewarakul P, Hoonsuwan T, Ruengjitchatchawalya M, Mekvichitsaeng P, Roshorm YM. Immunodominant linear B cell epitopes in the spike and membrane proteins of SARS-CoV-2 identified by immunoinformatics prediction and immunoassay. Sci Rep 2021; 11:20383. [PMID: 34650130 PMCID: PMC8516869 DOI: 10.1038/s41598-021-99642-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/29/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 continues to infect an ever-expanding number of people, resulting in an increase in the number of deaths globally. With the emergence of new variants, there is a corresponding decrease in the currently available vaccine efficacy, highlighting the need for greater insights into the viral epitope profile for both vaccine design and assessment. In this study, three immunodominant linear B cell epitopes in the SARS-CoV-2 spike receptor-binding domain (RBD) were identified by immunoinformatics prediction, and confirmed by ELISA with sera from Macaca fascicularis vaccinated with a SARS-CoV-2 RBD subunit vaccine. Further immunoinformatics analyses of these three epitopes gave rise to a method of linear B cell epitope prediction and selection. B cell epitopes in the spike (S), membrane (M), and envelope (E) proteins were subsequently predicted and confirmed using convalescent sera from COVID-19 infected patients. Immunodominant epitopes were identified in three regions of the S2 domain, one region at the S1/S2 cleavage site and one region at the C-terminus of the M protein. Epitope mapping revealed that most of the amino acid changes found in variants of concern are located within B cell epitopes in the NTD, RBD, and S1/S2 cleavage site. This work provides insights into B cell epitopes of SARS-CoV-2 as well as immunoinformatics methods for B cell epitope prediction, which will improve and enhance SARS-CoV-2 vaccine development against emergent variants.
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Affiliation(s)
- Kanokporn Polyiam
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Waranyoo Phoolcharoen
- Research Unit for Plant-Produced Pharmaceuticals and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Namphueng Butkhot
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chanya Srisaowakarn
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tawatchai Hoonsuwan
- B.F. Feed Company Limited, Prachachuen Road, Thung Song Hong, Lak Si, Bangkok, Thailand
| | - Marasri Ruengjitchatchawalya
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Phenjun Mekvichitsaeng
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Yaowaluck Maprang Roshorm
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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27
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Shehata MM, Mahmoud SH, Tarek M, Al-Karmalawy AA, Mahmoud A, Mostafa A, M. Elhefnawi M, Ali MA. In Silico and In Vivo Evaluation of SARS-CoV-2 Predicted Epitopes-Based Candidate Vaccine. Molecules 2021; 26:molecules26206182. [PMID: 34684763 PMCID: PMC8540548 DOI: 10.3390/molecules26206182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, the causative agent of coronavirus disease (COVID-19)) has caused relatively high mortality rates in humans throughout the world since its first detection in late December 2019, leading to the most devastating pandemic of the current century. Consequently, SARS-CoV-2 therapeutic interventions have received high priority from public health authorities. Despite increased COVID-19 infections, a vaccine or therapy to cover all the population is not yet available. Herein, immunoinformatics and custommune tools were used to identify B and T-cells epitopes from the available SARS-CoV-2 sequences spike (S) protein. In the in silico predictions, six B cell epitopes QTGKIADYNYK, TEIYQASTPCNGVEG, LQSYGFQPT, IRGDEVRQIAPGQTGKIADYNYKLPD, FSQILPDPSKPSKRS and PFAMQMAYRFNG were cross-reacted with MHC-I and MHC-II T-cells binding epitopes and selected for vaccination in experimental animals for evaluation as candidate vaccine(s) due to their high antigenic matching and conserved score. The selected six peptides were used individually or in combinations to immunize female Balb/c mice. The immunized mice raised reactive antibodies against SARS-CoV-2 in two different short peptides located in receptor binding domain and S2 region. In combination groups, an additive effect was demonstrated in-comparison with single peptide immunized mice. This study provides novel epitope-based peptide vaccine candidates against SARS-CoV-2.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/chemistry
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/metabolism
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Female
- Humans
- Immunization
- Mice
- Mice, Inbred BALB C
- Peptides/chemistry
- Peptides/immunology
- Peptides/metabolism
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Mahmoud M. Shehata
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (S.H.M.); (A.M.); (M.A.A.)
- Institute of Medical Virology, Justus Liebig University Giessen, 35392 Giessen, Germany
- Correspondence: or (M.M.S.); (A.M.)
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (S.H.M.); (A.M.); (M.A.A.)
| | - Mohammad Tarek
- Bioinformatics Department, Armed Forces College of Medicine (AFCM), Cairo 11757, Egypt;
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt;
| | - Amal Mahmoud
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box. 1982, Dammam 31441, Saudi Arabia
- Correspondence: or (M.M.S.); (A.M.)
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (S.H.M.); (A.M.); (M.A.A.)
| | - Mahmoud M. Elhefnawi
- National Research Centre, Biomedical Informatics and Cheminformatics Group, Informatics and Systems Department, Cairo 12622, Egypt;
| | - Mohamed A. Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (S.H.M.); (A.M.); (M.A.A.)
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28
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Fadaka AO, Sibuyi NRS, Martin DR, Goboza M, Klein A, Madiehe AM, Meyer M. Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus. Sci Rep 2021; 11:19707. [PMID: 34611250 PMCID: PMC8492693 DOI: 10.1038/s41598-021-99227-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/22/2021] [Indexed: 02/08/2023] Open
Abstract
Dengue poses a global health threat, which will persist without therapeutic intervention. Immunity induced by exposure to one serotype does not confer long-term protection against secondary infection with other serotypes and is potentially capable of enhancing this infection. Although vaccination is believed to induce durable and protective responses against all the dengue virus (DENV) serotypes in order to reduce the burden posed by this virus, the development of a safe and efficacious vaccine remains a challenge. Immunoinformatics and computational vaccinology have been utilized in studies of infectious diseases to provide insight into the host-pathogen interactions thus justifying their use in vaccine development. Since vaccination is the best bet to reduce the burden posed by DENV, this study is aimed at developing a multi-epitope based vaccines for dengue control. Combined approaches of reverse vaccinology and immunoinformatics were utilized to design multi-epitope based vaccine from the sequence of DENV. Specifically, BCPreds and IEDB servers were used to predict the B-cell and T-cell epitopes, respectively. Molecular docking was carried out using Schrödinger, PATCHDOCK and FIREDOCK. Codon optimization and in silico cloning were done using JCAT and SnapGene respectively. Finally, the efficiency and stability of the designed vaccines were assessed by an in silico immune simulation and molecular dynamic simulation, respectively. The predicted epitopes were prioritized using in-house criteria. Four candidate vaccines (DV-1-4) were designed using suitable adjuvant and linkers in addition to the shortlisted epitopes. The binding interactions of these vaccines against the receptors TLR-2, TLR-4, MHC-1 and MHC-2 show that these candidate vaccines perfectly fit into the binding domains of the receptors. In addition, DV-1 has a better binding energies of - 60.07, - 63.40, - 69.89 kcal/mol against MHC-1, TLR-2, and TLR-4, with respect to the other vaccines. All the designed vaccines were highly antigenic, soluble, non-allergenic, non-toxic, flexible, and topologically assessable. The immune simulation analysis showed that DV-1 may elicit specific immune response against dengue virus. Moreover, codon optimization and in silico cloning validated the expressions of all the designed vaccines in E. coli. Finally, the molecular dynamic study shows that DV-1 is stable with minimum RMSF against TLR4. Immunoinformatics tools are now applied to screen genomes of interest for possible vaccine target. The designed vaccine candidates may be further experimentally investigated as potential vaccines capable of providing definitive preventive measure against dengue virus infection.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Darius Riziki Martin
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mediline Goboza
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.
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Zhou F, Xu X, Cui X, Pan W. Development and Evaluation of a Fusion Polyprotein Based on HspX and Other Antigen Sequences for the Serodiagnosis of Tuberculosis. Front Immunol 2021; 12:726920. [PMID: 34671347 PMCID: PMC8521024 DOI: 10.3389/fimmu.2021.726920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background The lack of suitable diagnostic tools contributes to the high prevalence of tuberculosis (TB) worldwide. Serological tests, based on multiple target antigens, represent an attractive option for diagnosis of this disease due to their rapidity, convenience, and low cost. Methods Measures to reduce non-specific reactions and thereby improve the specificity of serological tests were investigated, including blocking antibodies against common bacteria in serum samples and synthesizing polypeptides covering non-conserved dominant B-cell epitopes of antigens. In addition, a fusion polyprotein containing HspX and eight other antigen sequences was constructed and expressed to increase overall sensitivity of the tests. Results Inclusion of Escherichia coli lysate partially increased the specificity of the serological tests, while synthesis and inclusion of peptides containing non-conserved sequences of TB antigens as well as dominant B-cell epitopes reduced non-specific reactions without a decrease in sensitivity of the tests. A polyprotein fusing HspX and eight other antigen sequences was constructed and displayed 60.2% sensitivity, which was higher than that of HspX and the other individual antigen segments. Moreover, the specificity of the polyprotein was 93.8%, which was not significantly decreased when compared with HspX and the other individual antigen segments. Conclusions The roles of the fusion polyprotein in the humoral immune response against TB infection were demonstrated and provide a potential novel approach for the development of TB diagnostics.
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Affiliation(s)
- Fangbin Zhou
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
- Clinical Medical Research Center, The Second Clinical Medical College, Shenzhen People’s Hospital, Jinan University, Shenzhen, China
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xiaobing Cui
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Weiqing Pan
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
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30
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Aljedani SS, Liban TJ, Tran K, Phad G, Singh S, Dubrovskaya V, Pushparaj P, Martinez-Murillo P, Rodarte J, Mileant A, Mangala Prasad V, Kinzelman R, O’Dell S, Mascola JR, Lee KK, Karlsson Hedestam GB, Wyatt RT, Pancera M. Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. PLoS Pathog 2021; 17:e1009543. [PMID: 34559844 PMCID: PMC8494329 DOI: 10.1371/journal.ppat.1009543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/06/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.
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Affiliation(s)
- Safia S. Aljedani
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Tyler J. Liban
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Karen Tran
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Ganesh Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Viktoriya Dubrovskaya
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Justas Rodarte
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Alex Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Rachel Kinzelman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Richard T. Wyatt
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
- * E-mail:
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31
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Rawal K, Sinha R, Abbasi BA, Chaudhary A, Nath SK, Kumari P, Preeti P, Saraf D, Singh S, Mishra K, Gupta P, Mishra A, Sharma T, Gupta S, Singh P, Sood S, Subramani P, Dubey AK, Strych U, Hotez PJ, Bottazzi ME. Identification of vaccine targets in pathogens and design of a vaccine using computational approaches. Sci Rep 2021; 11:17626. [PMID: 34475453 PMCID: PMC8413327 DOI: 10.1038/s41598-021-96863-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Antigen identification is an important step in the vaccine development process. Computational approaches including deep learning systems can play an important role in the identification of vaccine targets using genomic and proteomic information. Here, we present a new computational system to discover and analyse novel vaccine targets leading to the design of a multi-epitope subunit vaccine candidate. The system incorporates reverse vaccinology and immuno-informatics tools to screen genomic and proteomic datasets of several pathogens such as Trypanosoma cruzi, Plasmodium falciparum, and Vibrio cholerae to identify potential vaccine candidates (PVC). Further, as a case study, we performed a detailed analysis of the genomic and proteomic dataset of T. cruzi (CL Brenner and Y strain) to shortlist eight proteins as possible vaccine antigen candidates using properties such as secretory/surface-exposed nature, low transmembrane helix (< 2), essentiality, virulence, antigenic, and non-homology with host/gut flora proteins. Subsequently, highly antigenic and immunogenic MHC class I, MHC class II and B cell epitopes were extracted from top-ranking vaccine targets. The designed vaccine construct containing 24 epitopes, 3 adjuvants, and 4 linkers was analysed for its physicochemical properties using different tools, including docking analysis. Immunological simulation studies suggested significant levels of T-helper, T-cytotoxic cells, and IgG1 will be elicited upon administration of such a putative multi-epitope vaccine construct. The vaccine construct is predicted to be soluble, stable, non-allergenic, non-toxic, and to offer cross-protection against related Trypanosoma species and strains. Further, studies are required to validate safety and immunogenicity of the vaccine.
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Affiliation(s)
- Kamal Rawal
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India.
| | - Robin Sinha
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Bilal Ahmed Abbasi
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Amit Chaudhary
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Swarsat Kaushik Nath
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Priya Kumari
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - P Preeti
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Devansh Saraf
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Shachee Singh
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Kartik Mishra
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Pranjay Gupta
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Astha Mishra
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Trapti Sharma
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Srijanee Gupta
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Prashant Singh
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Shriya Sood
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Preeti Subramani
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Aman Kumar Dubey
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Ulrich Strych
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Peter J Hotez
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
| | - Maria Elena Bottazzi
- Texas Children's Hospital Center for Vaccine Development, Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Biology, Baylor University, Waco, TX, USA
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32
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Wei S, Shi D, Wu H, Sun H, Chen J, Feng L, Su M, Sun D. Identification of a novel B cell epitope on the nucleocapsid protein of porcine deltacoronavirus. Virus Res 2021; 302:198497. [PMID: 34217778 PMCID: PMC8481650 DOI: 10.1016/j.virusres.2021.198497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging coronavirus that causes vomiting, diarrhea, dehydration, and even death of piglets, resulting in significant losses to the pig industry worldwide. However, the epitopes of PDCoV remain largely unknown. In this study, a monoclonal antibody (mAb) against the PDCoV nucleocapsid (N) protein, termed 9G1, was prepared using the lymphocyte hybridoma technique, and was identified as a type IgG1 with a κ light chain and reacted with the native N protein of PDCoV. Furthermore, the epitope recognized by the 9G1 mAb was subjected to western blot and an ELISA using truncated recombinant proteins and synthetic polypeptides of the PDCoV N protein. The results indicate that 9G1 mAb recognized the epitope, G59TPIPPSYAFYY70 (EP-9G1), a novel linear B cell epitope of the PDCoV N protein. A comparison analysis revealed that the EP-9G1 epitope was highly conserved among PDCoV strains, in which four residues (G59-F68YY70) were observed among different coronavirus genera. These data demonstrate that the EP-9G1 epitope identified in this study provides some basic information for further characterization of the antigenic structure of the PDCoV N protein and has potential use for developing diagnostic reagents for PDCoV.
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Affiliation(s)
- Shan Wei
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Haoyang Wu
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Haibo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Mingjun Su
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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33
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Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Tortorici MA, Walls AC, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Dillen JR, Tucker H, Bassi J, Silacci-Fregni C, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E, Abdelnabi R, Foo SYC, Cameroni E, Stumpf S, Croll TI, Nix JC, Havenar-Daughton C, Piccoli L, Benigni F, Neyts J, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Virgin HW, Whelan SPJ, Veesler D, Corti D, Bloom JD, Snell G. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 2021; 597:97-102. [PMID: 34261126 PMCID: PMC9282883 DOI: 10.1038/s41586-021-03807-6] [Citation(s) in RCA: 293] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse sarbecoviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E128) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.
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MESH Headings
- Adult
- Aged
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- Broadly Neutralizing Antibodies/chemistry
- Broadly Neutralizing Antibodies/immunology
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/chemistry
- COVID-19 Vaccines/immunology
- Cell Line
- Cricetinae
- Cross Reactions/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Female
- Humans
- Immune Evasion/genetics
- Immune Evasion/immunology
- Male
- Mesocricetus
- Middle Aged
- Models, Molecular
- SARS-CoV-2/chemistry
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccinology
- COVID-19 Drug Treatment
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Fabrizia Zatta
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amin Addetia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dora Pinto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Martina Beltramello
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - William G Glass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Adam S Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Anna De Marco
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | | | | | | | | | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | | | - Matteo S Pizzuto
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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34
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Soltan MA, Eldeen MA, Elbassiouny N, Mohamed I, El-damasy DA, Fayad E, Abu Ali OA, Raafat N, Eid RA, Al-Karmalawy AA. Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus. Int J Mol Sci 2021; 22:ijms22179330. [PMID: 34502239 PMCID: PMC8431361 DOI: 10.3390/ijms22179330] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/05/2023] Open
Abstract
Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-3 and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Nada Elbassiouny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Ibrahim Mohamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Dalia A. El-damasy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Nermin Raafat
- Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha 12573, Saudi Arabia;
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
- Correspondence: ; Tel.: +20-109-214-7330
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35
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Pinheiro JR, Camilo dos Reis E, Souza RDSO, Rocha ALS, Suesdek L, Azevedo V, Tiwari S, Rocha BGS, Birbrair A, Méndez EC, Luiz WB, Amorim JH. Comparison of Neutralizing Dengue Virus B Cell Epitopes and Protective T Cell Epitopes With Those in Three Main Dengue Virus Vaccines. Front Immunol 2021; 12:715136. [PMID: 34489965 PMCID: PMC8417696 DOI: 10.3389/fimmu.2021.715136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022] Open
Abstract
The four serotypes of Dengue virus (DENV1-4) are arboviruses (arthropod-borne viruses) that belong to the Flavivirus genus, Flaviviridae family. They are the causative agents of an infectious disease called dengue, an important global public health problem with significant social-economic impact. Thus, the development of safe and effective dengue vaccines is a priority according to the World Health Organization. Only one anti-dengue vaccine has already been licensed in endemic countries and two formulations are under phase III clinical trials. In this study, we aimed to compare the main anti-dengue virus vaccines, DENGVAXIA®, LAV-TDV, and TAK-003, regarding their antigens and potential to protect. We studied the conservation of both, B and T cell epitopes involved in immunological control of DENV infection along with vaccine viruses and viral isolates. In addition, we assessed the population coverage of epitope sets contained in each vaccine formulation with regard to different human populations. As main results, we found that all three vaccines contain the main B cell epitopes involved in viral neutralization. Similarly, LAV-TDV and TAK-003 contain most of T cell epitopes involved in immunological protection, a finding not observed in DENGVAXIA®, which explains main limitations of the only licensed dengue vaccine. In summary, the levels of presence and absence of epitopes that are target for protective immune response in the three main anti-dengue virus vaccines are shown in this study. Our results suggest that investing in vaccines that contain the majority of epitopes involved in protective immunity (cellular and humoral arms) is an important issue to be considered.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Conserved Sequence
- Dengue/prevention & control
- Dengue Vaccines/genetics
- Dengue Vaccines/immunology
- Dengue Virus/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Humans
- Immunization Programs
- Models, Molecular
- Structure-Activity Relationship
- Vaccination
- Vaccines, Synthetic
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Affiliation(s)
- Josilene Ramos Pinheiro
- Laboratório de Agentes Infecciosos e Vetores, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
- Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
| | - Esther Camilo dos Reis
- Laboratório de Agentes Infecciosos e Vetores, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
| | - Rayane da Silva Oliveira Souza
- Laboratório de Agentes Infecciosos e Vetores, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
| | - Ana Luíza Silva Rocha
- Laboratório de Agentes Infecciosos e Vetores, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
| | - Lincoln Suesdek
- Laboratório de Parasitologia, Instituto, Butantan, São Paulo, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Alexander Birbrair
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Erick Carvalho Méndez
- Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
| | - Wilson Barros Luiz
- Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
| | - Jaime Henrique Amorim
- Laboratório de Agentes Infecciosos e Vetores, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Bahia, Brazil
- Programa de Pós-graduação em Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz, Bahia, Brazil
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36
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Yu M, Zhu Y, Li Y, Chen Z, Sha T, Li Z, Zhang F, Ding J. Design of a Novel Multi-Epitope Vaccine Against Echinococcus granulosus in Immunoinformatics. Front Immunol 2021; 12:668492. [PMID: 34456902 PMCID: PMC8388843 DOI: 10.3389/fimmu.2021.668492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022] Open
Abstract
All the time, echinococcosis is a global zoonotic disease which seriously endangers public health all over the world. In order to speed up the development process of anti-Echinococcus granulosus vaccine, at the same time, it can also save economic cost. In this study, immunoinformatics tools and molecular docking methods were used to predict and screen the antigen epitopes of Echinococcus granulosus, to design a multi-epitope vaccine containing B- and T-cell epitopes. The multi-epitope vaccine could activate B lymphocytes to produce specific antibodies theoretically, which could protect the human body against Echinococcus granulosus infection. It also could activate T lymphocytes and clear the infected parasites in the body. In this study, four CD8+ T-cell epitopes, three CD4+ T-cell epitopes and four B-cell epitopes of Protein EgTeg were identified by immunoinformatics methods. Meanwhile, three CD8+ T-cell epitopes, two CD4+ T-cell epitopes and four B-cell epitopes of Protein EgFABP1 were identified. We constructed the multi-epitope vaccine using linker proteins. The study based on the traditional methods of antigen epitope prediction, further optimized the prediction results combined with molecular docking technology and improved the precision and accuracy of the results. Finally, in vivo and in vitro experiments had verified that the vaccine designed in this study had good antigenicity and immunogenicity.
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MESH Headings
- Adolescent
- Adult
- Animals
- Antibodies, Helminth/blood
- Antigens, Helminth/immunology
- Antigens, Helminth/pharmacology
- B-Lymphocytes/immunology
- B-Lymphocytes/parasitology
- Cells, Cultured
- Computer-Aided Design
- Disease Models, Animal
- Drug Design
- Echinococcosis/blood
- Echinococcosis/immunology
- Echinococcosis/parasitology
- Echinococcosis/prevention & control
- Echinococcus granulosus/immunology
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/immunology
- Fatty Acid-Binding Proteins/immunology
- Fatty Acid-Binding Proteins/pharmacology
- Humans
- Immunity, Humoral
- Immunogenicity, Vaccine
- Lymphocyte Activation
- Mice, Inbred BALB C
- Middle Aged
- Molecular Docking Simulation
- T-Lymphocytes/immunology
- T-Lymphocytes/parasitology
- Vaccines, DNA/immunology
- Vaccines, DNA/pharmacology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/pharmacology
- Young Adult
- Mice
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Tong Sha
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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37
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Karami Fath M, Jahangiri A, Ganji M, Sefid F, Payandeh Z, Hashemi ZS, Pourzardosht N, Hessami A, Mard-Soltani M, Zakeri A, Rahbar MR, Khalili S. SARS-CoV-2 Proteome Harbors Peptides Which Are Able to Trigger Autoimmunity Responses: Implications for Infection, Vaccination, and Population Coverage. Front Immunol 2021; 12:705772. [PMID: 34447375 PMCID: PMC8383889 DOI: 10.3389/fimmu.2021.705772] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/23/2021] [Indexed: 12/16/2022] Open
Abstract
Autoimmune diseases (ADs) could occur due to infectious diseases and vaccination programs. Since millions of people are expected to be infected with SARS-CoV-2 and vaccinated against it, autoimmune consequences seem inevitable. Therefore, we have investigated the whole proteome of the SARS-CoV-2 for its ability to trigger ADs. In this regard, the entire proteome of the SARS-CoV-2 was chopped into more than 48000 peptides. The produced peptides were searched against the entire human proteome to find shared peptides with similar experimentally confirmed T-cell and B-cell epitopes. The obtained peptides were checked for their ability to bind to HLA molecules. The possible population coverage was calculated for the most potent peptides. The obtained results indicated that the SARS-CoV-2 and human proteomes share 23 peptides originated from ORF1ab polyprotein, nonstructural protein NS7a, Surface glycoprotein, and Envelope protein of SARS-CoV-2. Among these peptides, 21 peptides had experimentally confirmed equivalent epitopes. Amongst, only nine peptides were predicted to bind to HLAs with known global allele frequency data, and three peptides were able to bind to experimentally confirmed HLAs of equivalent epitopes. Given the HLAs which have already been reported to be associated with ADs, the ESGLKTIL, RYPANSIV, NVAITRAK, and RRARSVAS were determined to be the most harmful peptides of the SARS-CoV-2 proteome. It would be expected that the COVID-19 pandemic and the vaccination against this pathogen could significantly increase the ADs incidences, especially in populations harboring HLA-B*08:01, HLA-A*024:02, HLA-A*11:01 and HLA-B*27:05. The Southeast Asia, East Asia, and Oceania are at higher risk of AD development.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Sefid
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Sadat Hashemi
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maysam Mard-Soltani
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Dezful University of Medical Sciences, Dezful, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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38
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Cañas-Arranz R, de León P, Defaus S, Torres E, Forner M, Bustos MJ, Andreu D, Blanco E, Sobrino F. Immunogenicity of Foot-and-Mouth Disease Virus Dendrimer Peptides: Need for a T-Cell Epitope and Ability to Elicit Heterotypic Responses. Molecules 2021; 26:molecules26164714. [PMID: 34443302 PMCID: PMC8398643 DOI: 10.3390/molecules26164714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022] Open
Abstract
An approach based on a dendrimer display of B- and T-cell epitopes relevant for antibody induction has been shown to be effective as a foot-and-mouth disease (FMD) vaccine. B2T dendrimers combining two copies of the major FMD virus (FMDV) type O B-cell epitope (capsid proteinVP1 (140–158)) covalently linked to a heterotypic T-cell epitope from non-structural protein 3A (21–35), henceforth B2T-3A, has previously been shown to elicit high neutralizing antibody (nAb) titers and IFN-γ-producing cells in both mice and pigs. Here, we provide evidence that the B- and T-cell epitopes need to be tethered to a single molecular platform for successful T-cell help, leading to efficient nAb induction in mice. In addition, mice immunized with a non-covalent mixture of B2T-3A dendrimers containing the B-cell epitopes of FMDV types O and C induced similarly high nAb levels against both serotypes, opening the way for a multivalent vaccine platform against a variety of serologically different FMDVs. These findings are relevant for the design of vaccine strategies based on B- and T-cell epitope combinations.
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Affiliation(s)
- Rodrigo Cañas-Arranz
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.)
| | - Patricia de León
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.)
| | - Sira Defaus
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (S.D.); (M.F.); (D.A.)
| | - Elisa Torres
- Centro de Investigación en Sanidad Animal (CISA-INIA), 28130 Valdeolmos, Spain; (E.T.); (E.B.)
| | - Mar Forner
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (S.D.); (M.F.); (D.A.)
| | - María J. Bustos
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.)
| | - David Andreu
- Departament de Ciències Experimentals i de la Salut (DCEXS-UPF), 08003 Barcelona, Spain; (S.D.); (M.F.); (D.A.)
| | - Esther Blanco
- Centro de Investigación en Sanidad Animal (CISA-INIA), 28130 Valdeolmos, Spain; (E.T.); (E.B.)
| | - Francisco Sobrino
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.)
- Correspondence:
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39
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Gu Y, Merriman C, Guo Z, Jia X, Wenzlau J, Li H, Li H, Rewers M, Yu L, Fu D. Novel autoantibodies to the β-cell surface epitopes of ZnT8 in patients progressing to type-1 diabetes. J Autoimmun 2021; 122:102677. [PMID: 34130115 PMCID: PMC9029399 DOI: 10.1016/j.jaut.2021.102677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 11/22/2022]
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by autoimmune destruction of insulin-producing β-cells in pancreatic islets. Seroconversions to islet autoantibodies (IAbs) precede the disease onset by many years, but the role of humoral autoimmunity in the disease initiation and progression are unclear. In the present study, we identified a new IAb directed to the extracellular epitopes of ZnT8 (ZnT8ec) in newly diagnosed patients with T1D, and demonstrated immunofluorescence staining of the surface of human β-cells by autoantibodies to ZnT8ec (ZnT8ecA). With the assay specificity set on 99th percentile of 336 healthy controls, the ZnT8ecA positivity rate was 23.6% (74/313) in patients with T1D. Moreover, 30 children in a longitudinal follow up of clinical T1D development were selected for sequential expression of four major IAbs (IAA, GADA, IA-2A and ZnT8icA). Among them, 10 children were ZnT8ecA positive. Remarkably, ZnT8ecA was the earliest IAb to appear in all 10 children. The identification of ZnT8ec as a cell surface target of humoral autoimmunity in the earliest phase of IAb responses opens a new avenue of investigation into the role of IAbs in the development of β-cell autoimmunity.
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Affiliation(s)
- Yong Gu
- Barbara Davis Center for Diabetes University of Colorado School of Medicine, Aurora, CO, USA
| | - Chengfeng Merriman
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Zheng Guo
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Xiaofan Jia
- Barbara Davis Center for Diabetes University of Colorado School of Medicine, Aurora, CO, USA
| | - Janet Wenzlau
- Barbara Davis Center for Diabetes University of Colorado School of Medicine, Aurora, CO, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes University of Colorado School of Medicine, Aurora, CO, USA
| | - Liping Yu
- Barbara Davis Center for Diabetes University of Colorado School of Medicine, Aurora, CO, USA.
| | - Dax Fu
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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40
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Chen X, Ding X, Zhu L, Zhang G. The identification of a B-cell epitope in bovine viral diarrhea virus (BVDV) core protein based on a mimotope obtained from a phage-displayed peptide library. Int J Biol Macromol 2021; 183:2376-2386. [PMID: 34111485 DOI: 10.1016/j.ijbiomac.2021.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 01/03/2023]
Abstract
Bovine pestivirus A and B, previously known as bovine viral diarrhea virus (BVDV)-1 and 2, respectively, are important pathogens of cattle worldwide, which causes significant economic losses. B-cell epitopes in BVDV glycoprotein E2 and nonstructural protein NS2/3 have been extensively identified. In this study, we screened a 12-mer phage display peptide library using commercial goat anti-BVDV serum, and identified a mimotope "LTPHKHHKHLHA" referred to as P3. With sequence alignment, a putative B-cell epitope "77ESRKKLEKALLA88" termed as P3-BVDV1/2 residing in BVDV core protein was identified. The synthesized peptides of both P3 and P3-BVDV1/2 show strong reactivity with BVDV serum in immune blot assay. Immunization of mice with these individual peptides leads to the production of antibody that cannot neutralize virus infectivity. Thus for the first time we identified a B-cell epitope, "77ESRKKLEKALLA88", in BVDV core protein. Interestingly, the epitope was highly conserved in Pestivirus A, B, C, D, as well as emerging Pestivirus E and I, but highly variable in Pestiviruses H, G, F, and J, as well as unclassified Pestivirus originated from non-ruminant animals. Whether this putative B-cell epitope is implicated in pestivirus pathogenesis or evolution needs further investigations once large numbers of isolates are available in the future.
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MESH Headings
- Animals
- Antibodies, Viral/blood
- Cattle
- Cell Surface Display Techniques
- Diarrhea Virus 1, Bovine Viral/genetics
- Diarrhea Virus 1, Bovine Viral/immunology
- Diarrhea Virus 1, Bovine Viral/pathogenicity
- Diarrhea Virus 2, Bovine Viral/genetics
- Diarrhea Virus 2, Bovine Viral/immunology
- Diarrhea Virus 2, Bovine Viral/pathogenicity
- Dogs
- Epitope Mapping
- Epitopes, B-Lymphocyte/administration & dosage
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Female
- Immunization
- Immunogenicity, Vaccine
- Madin Darby Canine Kidney Cells
- Mice, Inbred BALB C
- Mutation
- Peptide Library
- Viral Core Proteins/administration & dosage
- Viral Core Proteins/genetics
- Viral Core Proteins/immunology
- Viral Vaccines/administration & dosage
- Viral Vaccines/genetics
- Viral Vaccines/immunology
- Mice
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Affiliation(s)
- Xinye Chen
- College of Life Sciences, Hebei University, Baoding 071002, China; College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiuyan Ding
- College of Life Sciences, Hebei University, Baoding 071002, China; College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Liqian Zhu
- College of Life Sciences, Hebei University, Baoding 071002, China; College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| | - Gaiping Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450002, China; Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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41
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Salleh MZ, Derrick JP, Deris ZZ. Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion. Int J Mol Sci 2021; 22:7425. [PMID: 34299045 PMCID: PMC8306177 DOI: 10.3390/ijms22147425] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Mohd Zulkifli Salleh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
| | - Jeremy P. Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PL, UK;
| | - Zakuan Zainy Deris
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
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42
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Voss C, Esmail S, Liu X, Knauer MJ, Ackloo S, Kaneko T, Lowes L, Stogios P, Seitova A, Hutchinson A, Yusifov F, Skarina T, Evdokimova E, Loppnau P, Ghiabi P, Haijan T, Zhong S, Abdoh H, Hedley BD, Bhayana V, Martin CM, Slessarev M, Chin-Yee B, Fraser DD, Chin-Yee I, Li SS. Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. JCI Insight 2021; 6:148855. [PMID: 34081630 PMCID: PMC8410046 DOI: 10.1172/jci.insight.148855] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUNDThe role of humoral immunity in COVID-19 is not fully understood, owing, in large part, to the complexity of antibodies produced in response to the SARS-CoV-2 infection. There is a pressing need for serology tests to assess patient-specific antibody response and predict clinical outcome.METHODSUsing SARS-CoV-2 proteome and peptide microarrays, we screened 146 COVID-19 patients' plasma samples to identify antigens and epitopes. This enabled us to develop a master epitope array and an epitope-specific agglutination assay to gauge antibody responses systematically and with high resolution.RESULTSWe identified linear epitopes from the spike (S) and nucleocapsid (N) proteins and showed that the epitopes enabled higher resolution antibody profiling than the S or N protein antigen. Specifically, we found that antibody responses to the S-811-825, S-881-895, and N-156-170 epitopes negatively or positively correlated with clinical severity or patient survival. Moreover, we found that the P681H and S235F mutations associated with the coronavirus variant of concern B.1.1.7 altered the specificity of the corresponding epitopes.CONCLUSIONEpitope-resolved antibody testing not only affords a high-resolution alternative to conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, but it also may potentially be used to predict clinical outcome. The epitope peptides can be readily modified to detect antibodies against variants of concern in both the peptide array and latex agglutination formats.FUNDINGOntario Research Fund (ORF) COVID-19 Rapid Research Fund, Toronto COVID-19 Action Fund, Western University, Lawson Health Research Institute, London Health Sciences Foundation, and Academic Medical Organization of Southwestern Ontario (AMOSO) Innovation Fund.
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MESH Headings
- Agglutination Tests/methods
- Amino Acid Sequence
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antibody Formation/immunology
- Antibody Specificity/immunology
- COVID-19/blood
- COVID-19/immunology
- COVID-19/mortality
- COVID-19 Serological Testing/methods
- Epitopes/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Humans
- Immunity, Humoral
- Microarray Analysis/methods
- Nucleocapsid/chemistry
- Nucleocapsid/genetics
- Nucleocapsid/immunology
- Peptides/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Severity of Illness Index
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
| | | | | | - Michael J. Knauer
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | | | - Lori Lowes
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Pegah Ghiabi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Taraneh Haijan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Husam Abdoh
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Benjamin D. Hedley
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Vipin Bhayana
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Claudio M. Martin
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | - Marat Slessarev
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | | | - Douglas D. Fraser
- Department of Medicine, Western University, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
- Department of Paediatrics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
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43
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Zhu L, Zhang Y, Yang Z, Li B, Feng T, Zou X, He J, He T, Li J, Liu N, Li W, Wang X. Seropositive reaction rates of 9 B cell epitopes of the SARS-CoV-2 spike protein and the relationship between the epitopes and neutralizing antibody. Intervirology 2021; 65:29-36. [PMID: 34233324 DOI: 10.1159/000517717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Li Zhu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yunwen Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhengrong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Tiejian Feng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xuan Zou
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jianfan He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Taiping He
- School of Public Health, Guangdong Medical University, Zhanjiang, China
| | - Junling Li
- School of Public Health, Guangdong Medical University, Zhanjiang, China
| | - Ning Liu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Wei Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaohui Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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44
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Asghari A, Nourmohammadi H, Majidiani H, Shariatzadeh SA, Shams M, Montazeri F. In silico analysis and prediction of immunogenic epitopes for pre-erythrocytic proteins of the deadly Plasmodium falciparum. Infect Genet Evol 2021; 93:104985. [PMID: 34214673 DOI: 10.1016/j.meegid.2021.104985] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 12/18/2022]
Abstract
Malaria is the deadliest parasitic disease in tropical and subtropical areas around the world, with considerable morbidity and mortality, particularly due to the life-threatening Plasmodium falciparum. The present in silico investigation was performed to reveal the biophysical characteristics and immunogenic epitopes of the six pre-erythrocytic proteins of the P. falciparum using comprehensive immunoinformatics approaches. For this aim, different web servers were employed to predict subcellular localization, antigenicity, allergenicity, solubility, physico-chemical properties, post-translational modification sites (PTMs), the presence of signal peptide and transmembrane domains. Moreover, the secondary and tertiary structures of the proteins were revealed followed by refinement and validations. Finally, NetCTL server was used to predict cytotoxic T-lymphocyte (CTL) epitopes, followed by subsequent screening in terms of antigenicity and immunogenicity. Also, IEDB server was utilized to predict helper T-lymphocyte (HTL) epitopes, followed by screening regarding interferon gamma induction and population coverage. These proteins showed appropriate antigenicity, abundant PTMs as well as many CTL and HTL epitopes, which could be directed for future vaccination studies in the context of multi-epitope vaccine design.
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Affiliation(s)
- Ali Asghari
- Department of Medical Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Nourmohammadi
- Department of Internal Medicine, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran; Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Hamidreza Majidiani
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Seyyed Ali Shariatzadeh
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Morteza Shams
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran; Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran.
| | - Fattaneh Montazeri
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Leung LYT, Khan S, Budylowski P, Li Z, Goroshko S, Liu Y, Dong S, Carlyle JR, Rini JM, Ostrowski M, Ehrhardt GRA. Detection and Neutralization of SARS-CoV-2 Using Non-conventional Variable Lymphocyte Receptor Antibodies of the Evolutionarily Distant Sea Lamprey. Front Immunol 2021; 12:659071. [PMID: 34234774 PMCID: PMC8256154 DOI: 10.3389/fimmu.2021.659071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is a newly emerged betacoronavirus and the causative agent for the COVID-19 pandemic. Antibodies recognizing the viral spike protein are instrumental in natural and vaccine-induced immune responses to the pathogen and in clinical diagnostic and therapeutic applications. Unlike conventional immunoglobulins, the variable lymphocyte receptor antibodies of jawless vertebrates are structurally distinct, indicating that they may recognize different epitopes. Here we report the isolation of monoclonal variable lymphocyte receptor antibodies from immunized sea lamprey larvae that recognize the spike protein of SARS-CoV-2 but not of other coronaviruses. We further demonstrate that these monoclonal variable lymphocyte receptor antibodies can efficiently neutralize the virus and form the basis of a rapid, single step SARS-CoV-2 detection system. This study provides evidence for monoclonal variable lymphocyte receptor antibodies as unique biomedical research and potential clinical diagnostic reagents targeting SARS-CoV-2.
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Affiliation(s)
| | - Srijit Khan
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Zhijie Li
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sofiya Goroshko
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Shilan Dong
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - James R. Carlyle
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - James M. Rini
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
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Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O'Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med 2021; 13:101. [PMID: 34127050 PMCID: PMC8201469 DOI: 10.1186/s13073-021-00910-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). METHODS We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. RESULTS From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. CONCLUSIONS Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kelly S Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kaylee M Gentry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Allison Woods
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Brandon Carpenter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Sandor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
- Institute for Inflammatory Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Division of Medical Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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Deshpande A, Harris BD, Martinez-Sobrido L, Kobie JJ, Walter MR. Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Front Immunol 2021; 12:691715. [PMID: 34149735 PMCID: PMC8212047 DOI: 10.3389/fimmu.2021.691715] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/21/2021] [Indexed: 11/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SAR-CoV-2) causes coronavirus disease 2019 (COVID19) that is responsible for short and long-term disease, as well as death, in susceptible hosts. The receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) protein binds to cell surface angiotensin converting enzyme type-II (ACE2) to initiate viral attachment and ultimately viral pathogenesis. The SARS-CoV-2 S RBD is a major target of neutralizing antibodies (NAbs) that block RBD - ACE2 interactions. In this report, NAb-RBD binding epitopes in the protein databank were classified as C1, C1D, C2, C3, or C4, using a RBD binding profile (BP), based on NAb-specific RBD buried surface area and used to predict the binding epitopes of a series of uncharacterized NAbs. Naturally occurring SARS-CoV-2 RBD sequence variation was also quantified to predict NAb binding sensitivities to the RBD-variants. NAb and ACE2 binding studies confirmed the NAb classifications and determined whether the RBD variants enhanced ACE2 binding to promote viral infectivity, and/or disrupted NAb binding to evade the host immune response. Of 9 single RBD mutants evaluated, K417T, E484K, and N501Y disrupted binding of 65% of the NAbs evaluated, consistent with the assignment of the SARS-CoV-2 P.1 Japan/Brazil strain as a variant of concern (VoC). RBD variants E484K and N501Y exhibited ACE2 binding equivalent to a Wuhan-1 reference SARS-CoV-2 RBD. While slightly less disruptive to NAb binding, L452R enhanced ACE2 binding affinity. Thus, the L452R mutant, associated with the SARS-CoV-2 California VoC (B.1.427/B.1.429-California), has evolved to enhance ACE2 binding, while simultaneously disrupting C1 and C2 NAb classes. The analysis also identified a non-overlapping antibody pair (1213H7 and 1215D1) that bound to all SARS-CoV-2 RBD variants evaluated, representing an excellent therapeutic option for treatment of SARS-CoV-2 WT and VoC strains.
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Affiliation(s)
- Ashlesha Deshpande
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bethany D. Harris
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - James J. Kobie
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Mark R. Walter,
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Dar HA, Ismail S, Waheed Y, Ahmad S, Jamil Z, Aziz H, Hetta HF, Muhammad K. Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology. Sci Rep 2021; 11:11197. [PMID: 34045649 PMCID: PMC8159972 DOI: 10.1038/s41598-021-90868-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Mycobacteroides abscessus (Previously Mycobacterium abscessus) is an emerging microorganism of the newly defined genera Mycobacteroides that causes mainly skin and tissue diseases in humans. The recent availability of total 34 fully sequenced genomes of different strains belonging to this species has provided an opportunity to utilize this genomics data to gain novel insights and guide the development of specific antimicrobial therapies. In the present study, we collected collectively 34 complete genome sequences of M. abscessus from the NCBI GenBank database. Pangenome analysis was conducted on these genomes to understand the genetic diversity and to obtain proteins associated with its core genome. These core proteins were then subjected to various subtractive filters to identify potential antigenic targets that were subjected to multi-epitope vaccine design. Our analysis projected the open pangenome of M. abscessus containing 3443 core genes. After applying various stepwise filtration steps on the core proteins, a total of four potential antigenic targets were identified. Utilizing their constituent CD4 and CD8 T-cell epitopes, a multi-epitope based subunit vaccine was computationally designed. Sequence-based analysis as well as structural characterization revealed the immunological effectiveness of this designed vaccine. Further molecular docking, molecular dynamics simulation and binding free energy estimation with Toll-like receptor 2 indicated strong structural associations of the vaccine with the immune receptor. The promising results are encouraging and need to be validated by additional wet laboratory studies for confirmation.
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Affiliation(s)
- Hamza Arshad Dar
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Saba Ismail
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan.
| | - Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Zubia Jamil
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000, Pakistan
| | - Hafsa Aziz
- Nuclear Medicine, Oncology, and Radiotherapy Institute, Islamabad, 44000, Pakistan
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, 71515, Egypt
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates.
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Ezaj MMA, Haque MS, Syed SB, Khan MSA, Ahmed KR, Khatun MT, Nayeem SMA, Rizvi GR, Al-Forkan M, Khaleda L. Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination. PLoS One 2021; 16:e0252295. [PMID: 34043709 PMCID: PMC8159010 DOI: 10.1371/journal.pone.0252295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant bacterium with no precise clinical treatment. This bacterium can be a vital cause for death and different organ failures in immune-compromised, immune-competent, and long-time hospitalized patients. Extensive quorum sensing capability has become a challenge to develop new drugs against this pathogen. Moreover, the organism possesses about 789 proteins which function, structure, and pathogenesis remain obscured. In this piece of work, we tried to enlighten the aforementioned sectors using highly reliable bioinformatics tools validated by the scientific community. At first, the whole proteome sequence of the organism was retrieved and stored. Then we separated the hypothetical proteins and searched for the conserved domain with a high confidence level and multi-server validation, which resulted in 24 such proteins. Furthermore, all of their physical and chemical characterizations were performed, such as theoretical isoelectric point, molecular weight, GRAVY value, and many more. Besides, the subcellular localization, protein-protein interactions, functional motifs, 3D structures, antigenicity, and virulence factors were also evaluated. As an extension of this work, 'RTFAMSSER' and 'PAAPQPSAS' were predicted as potential T and B cell epitopes, respectively. We hope our findings will help in better understating the pathogenesis and smoothen the way to the cure.
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Affiliation(s)
- Md. Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chittagong, Bangladesh
| | - Md. Sajedul Haque
- Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, Bangladesh
| | - Shifath Bin Syed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md. Shakil Ahmed Khan
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Kazi Rejvee Ahmed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst. Tania Khatun
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - S. M. Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chittagong, Bangladesh
- Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, Bangladesh
| | - Golam Rosul Rizvi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Al-Forkan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Laila Khaleda
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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50
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Guthmiller JJ, Utset HA, Wilson PC. B Cell Responses against Influenza Viruses: Short-Lived Humoral Immunity against a Life-Long Threat. Viruses 2021; 13:965. [PMID: 34067435 PMCID: PMC8224597 DOI: 10.3390/v13060965] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/25/2022] Open
Abstract
Antibodies are critical for providing protection against influenza virus infections. However, protective humoral immunity against influenza viruses is limited by the antigenic drift and shift of the major surface glycoproteins, hemagglutinin and neuraminidase. Importantly, people are exposed to influenza viruses throughout their life and tend to reuse memory B cells from prior exposure to generate antibodies against new variants. Despite this, people tend to recall memory B cells against constantly evolving variable epitopes or non-protective antigens, as opposed to recalling them against broadly neutralizing epitopes of hemagglutinin. In this review, we discuss the factors that impact the generation and recall of memory B cells against distinct viral antigens, as well as the immunological limitations preventing broadly neutralizing antibody responses. Lastly, we discuss how next-generation vaccine platforms can potentially overcome these obstacles to generate robust and long-lived protection against influenza A viruses.
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Affiliation(s)
- Jenna J. Guthmiller
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (H.A.U.); (P.C.W.)
| | - Henry A. Utset
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (H.A.U.); (P.C.W.)
| | - Patrick C. Wilson
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (H.A.U.); (P.C.W.)
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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