1
|
Ghafouri F, Ahangari Cohan R, Samimi H, Hosseini Rad S M A, Naderi M, Noorbakhsh F, Haghpanah V. Development of a Multiepitope Vaccine Against SARS-CoV-2: Immunoinformatics Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e36100. [PMID: 35891920 PMCID: PMC9302570 DOI: 10.2196/36100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]
Abstract
Background Since the first appearance of SARS-CoV-2 in China in December 2019, the world witnessed the emergence of the SARS-CoV-2 outbreak. Due to the high transmissibility rate of the virus, there is an urgent need to design and develop vaccines against SARS-CoV-2 to prevent more cases affected by the virus. Objective A computational approach is proposed for vaccine design against the SARS-CoV-2 spike (S) protein, as the key target for neutralizing antibodies, and envelope (E) protein, which contains a conserved sequence feature. Methods We used previously reported epitopes of S protein detected experimentally and further identified a collection of predicted B-cell and major histocompatibility (MHC) class II–restricted T-cell epitopes derived from E proteins with an identical match to SARS-CoV-2 E protein. Results The in silico design of our candidate vaccine against the S and E proteins of SARS-CoV-2 demonstrated a high affinity to MHC class II molecules and effective results in immune response simulations. Conclusions Based on the results of this study, the multiepitope vaccine designed against the S and E proteins of SARS-CoV-2 may be considered as a new, safe, and efficient approach to combatting the COVID-19 pandemic.
Collapse
Affiliation(s)
- Fatemeh Ghafouri
- Department of Biotechnology Faculty of Life Sciences and Biotechnology Shahid Beheshti University Tehran Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology New Technologies Research Group Pasteur Institute of Iran Tehran Iran
| | - Hilda Samimi
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
| | | | - Mahmood Naderi
- Digestive Diseases Research Center Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran
| | - Farshid Noorbakhsh
- Department of Immunology School of Medicine Tehran University of Medical Sciences Tehran Iran
| | - Vahid Haghpanah
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
- Personalized Medicine Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
| |
Collapse
|
2
|
Zhuang Z, Liu D, Sun J, Li F, Zhao J. Immune responses to human respiratory coronaviruses infection in mouse models. Curr Opin Virol 2021; 52:102-111. [PMID: 34906757 PMCID: PMC8665230 DOI: 10.1016/j.coviro.2021.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022]
Abstract
Human respiratory coronaviruses (HCoVs), including the recently emerged SARS-CoV-2, the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, potentially cause severe lung infections and multiple organ damages, emphasizing the urgent need for antiviral therapeutics and vaccines against HCoVs. Small animal models, especially mice, are ideal tools for deciphering the pathogenesis of HCoV infections as well as virus-induced immune responses, which is critical for antiviral drug development and vaccine design. In this review, we focus on the antiviral innate immune response, antibody response and T cell response in HCoV infected mouse models, and discuss the potential implications for understanding the anti-HCoV immunity and fighting the COVID-19 pandemic.
Collapse
Affiliation(s)
- Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China; Guangzhou Laboratory, Bio-Island, Guangzhou, Guangdong 510320, China.
| |
Collapse
|
3
|
Zhao L, Han N, Zheng Y, Rao H, Li J, Chen Y, Yu B, Xu Y, Chen H, Gao Z, Jiang B. Detection of Antibodies Against the SARS-CoV-2 Spike Protein and Analysis of the Peripheral Blood Mononuclear Cell Transcriptomic Profile, 15 Years After Recovery From SARS. Front Cell Infect Microbiol 2021; 11:768993. [PMID: 34869070 PMCID: PMC8636717 DOI: 10.3389/fcimb.2021.768993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shows a high degree of homology with SARS-CoV. They share genes, protein sequences, clinical manifestations, and cellular entry patterns. Thus, SARS research may serve helpful in gaining a better understanding of the current coronavirus disease 2019 (COVID-19) pandemic. Serum antibodies from convalescent patients with SARS collected in 2018 were used to target the recombinant SARS-CoV-2 spike protein via a chemiluminescence microsphere immunoassay. Antibodies of convalescent patients with SARS exhibited serous immune cross-reactivity with the SARS-CoV-2 spike protein. The serous antibodies, excluding S22 of convalescent patients with SARS, did not competitively inhibit the binding of SARS-CoV-2 spike protein to ACE2. T cellular immunity research was conducted in vitro using peripheral blood mononuclear cells (PBMCs) stimulated by pooled peptide epitopes 15 years post-infection. Interferon gamma was detected and the PBMC transcriptomic profile was obtained. The heatmap of the transcriptomic profile showed that mRNAs and circRNAs of the SARS group clustered together after being stimulated by the peptide epitope pool. Differentially expressed mRNAs were most significantly enriched in immunity and signal transduction (P < 0.01). SARS elicits cytokine and chemokine responses, partially consistent with previously published data about COVID-19. Overall, our results indicate that antibodies from convalescent patients with SARS persisted for 15 years and displayed immune cross-reactivity with the SARS-CoV-2 spike protein. The immune status of patients with SARS 15 years post-infection may provide a better understanding of the future immune status of patients with COVID-19.
Collapse
Affiliation(s)
- Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Na Han
- Department of Central Laboratory, Peking University People's Hospital, Beijing, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Xiang'An Hospital of Xiamen University, Xiamen, China
| | - Huiying Rao
- Peking University Hepatology Institute and Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Peking University People's Hospital, Beijing, China
| | - Jia Li
- Department of Emergency Medicine, Peking University People's Hospital, Beijing, China
| | - Yanwen Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Bing Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Hongsong Chen
- Peking University Hepatology Institute and Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Peking University People's Hospital, Beijing, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Baoguo Jiang
- Department of Orthopedics and Trauma, Peking University People's Hospital, Beijing, China
| |
Collapse
|
4
|
Thura M, Sng J, Ang K, Li J, Gupta A, Hong J, Hong C, Zeng Q. Targeting intra-viral conserved nucleocapsid (N) proteins as novel vaccines against SARS-CoVs. Biosci Rep 2021; 41:BSR20211491. [PMID: 34519332 PMCID: PMC8463655 DOI: 10.1042/bsr20211491] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global pandemic of the Coronavirus disease in late 2019 (COVID-19). Vaccine development efforts have predominantly been aimed at 'Extra-viral' Spike (S) protein as vaccine vehicles, but there are concerns regarding 'viral immune escape' since multiple mutations may enable the mutated virus strains to escape from immunity against S protein. The 'Intra-viral' Nucleocapsid (N-protein) is relatively conserved among mutant strains of coronaviruses during spread and evolution. Herein, we demonstrate novel vaccine candidates against SARS-CoV-2 by using the whole conserved N-protein or its fragment/peptides. Using ELISA assay, we showed that high titers of specific anti-N antibodies (IgG, IgG1, IgG2a, IgM) were maintained for a reasonably long duration (> 5 months), suggesting that N-protein is an excellent immunogen to stimulate host immune system and robust B-cell activation. We synthesized three peptides located at the conserved regions of N-protein among CoVs. One peptide showed as a good immunogen for vaccination as well. Cytokine arrays on post-vaccination mouse sera showed progressive up-regulation of various cytokines such as IFN-γ and CCL5, suggesting that TH1 associated responses are also stimulated. Furthermore, vaccinated mice exhibited an elevated memory T cells population. Here, we propose an unconventional vaccine strategy targeting the conserved N-protein as an alternative vaccine target for coronaviruses. Moreover, we generated a mouse monoclonal antibody specifically against an epitope shared between SARS-CoV and SARS-CoV-2, and we are currently developing the First-in-Class humanized anti-N-protein antibody to potentially treat patients infected by various CoVs in the future.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal, Murine-Derived
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/immunology
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunogenicity, Vaccine
- Mice
- Models, Animal
- Pandemics/prevention & control
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/immunology
- Th1 Cells/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
Collapse
Affiliation(s)
- Min Thura
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Joel Xuan En Sng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Koon Hwee Ang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Jie Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | - Abhishek Gupta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
| | | | - Cheng William Hong
- Department of Radiology, University of California San Diego, San Diego, CA 92103, USA
| | - Qi Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260
- INTRA-ImmuSG Private Limited, Singapore 079903
| |
Collapse
|
5
|
Chakraborty S, Mallajosyula V, Tato CM, Tan GS, Wang TT. SARS-CoV-2 vaccines in advanced clinical trials: Where do we stand? Adv Drug Deliv Rev 2021; 172:314-338. [PMID: 33482248 PMCID: PMC7816567 DOI: 10.1016/j.addr.2021.01.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
The ongoing SARS-CoV-2 pandemic has led to the focused application of resources and scientific expertise toward the goal of developing investigational vaccines to prevent COVID-19. The highly collaborative global efforts by private industry, governments and non-governmental organizations have resulted in a number of SARS-CoV-2 vaccine candidates moving to Phase III trials in a period of only months since the start of the pandemic. In this review, we provide an overview of the preclinical and clinical data on SARS-CoV-2 vaccines that are currently in Phase III clinical trials and in few cases authorized for emergency use. We further discuss relevant vaccine platforms and provide a discussion of SARS-CoV-2 antigens that may be targeted to increase the breadth and durability of vaccine responses.
Collapse
Affiliation(s)
- Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Cristina M Tato
- Infectious Disease Initiative, Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gene S Tan
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; Department of Infectious Diseases, University of California San Diego, La Jolla, CA 92037, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
6
|
Khan MT, Islam MJ, Parihar A, Islam R, Jerin TJ, Dhote R, Ali MA, Laura FK, Halim MA. Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021; 24:100578. [PMID: 33898733 PMCID: PMC8057924 DOI: 10.1016/j.imu.2021.100578] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmittable and pathogenic human coronavirus that caused a pandemic situation of acute respiratory syndrome, called COVID-19, which has posed a significant threat to global health security. The aim of the present study is to computationally design an effective peptide-based multi-epitope vaccine (MEV) against SARS-CoV-2. The overall model quality of the vaccine candidate, immunogenicity, allergenicity, and physiochemical analysis have been conducted and validated. Molecular dynamics studies confirmed the stability of the candidate vaccine. The docked complexes during the simulation revealed a strong and stable binding interactions of MEV with human and mice toll-like receptors (TLR), TLR3 and TLR4. Finally, candidate vaccine codons have been optimized for their in silico cloning in E. coli expression system, to confirm increased expression. The proposed MEV can be a potential candidate against SARS-CoV-2, but experimental validation is needed to ensure its safety and immunogenicity status.
Collapse
Affiliation(s)
- Md Tahsin Khan
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Arpana Parihar
- Department of Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rahatul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tarhima Jahan Jerin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Rupali Dhote
- Department of Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Md Ackas Ali
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Fariha Khan Laura
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammad A Halim
- Division of Infectious Diseases, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA
| |
Collapse
|
7
|
Zhuang Z, Lai X, Sun J, Chen Z, Zhang Z, Dai J, Liu D, Li Y, Li F, Wang Y, Zhu A, Wang J, Yang W, Huang J, Li X, Hu L, Wen L, Zhuo J, Zhang Y, Chen D, Li S, Huang S, Shi Y, Zheng K, Zhong N, Zhao J, Zhou D, Zhao J. Mapping and role of T cell response in SARS-CoV-2-infected mice. J Exp Med 2021; 218:e20202187. [PMID: 33464307 PMCID: PMC7814348 DOI: 10.1084/jem.20202187] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/06/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
Virus-specific T cells play essential roles in protection against multiple virus infections, including SARS-CoV and MERS-CoV. While SARS-CoV-2-specific T cells have been identified in COVID-19 patients, their role in the protection of SARS-CoV-2-infected mice is not established. Here, using mice sensitized for infection with SARS-CoV-2 by transduction with an adenovirus expressing the human receptor (Ad5-hACE2), we identified SARS-CoV-2-specific T cell epitopes recognized by CD4+ and CD8+ T cells in BALB/c and C57BL/6 mice. Virus-specific T cells were polyfunctional and were able to lyse target cells in vivo. Further, type I interferon pathway was proved to be critical for generating optimal antiviral T cell responses after SARS-CoV-2 infection. T cell vaccination alone partially protected SARS-CoV-2-infected mice from severe disease. In addition, the results demonstrated cross-reactive T cell responses between SARS-CoV and SARS-CoV-2, but not MERS-CoV, in mice. Understanding the role of the T cell response will guide immunopathogenesis studies of COVID-19 and vaccine design and validation.
Collapse
Affiliation(s)
- Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaomin Lai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuming Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jicheng Huang
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Xiaobo Li
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liyan Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dingbin Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Suxiang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuxiang Huang
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Yongxia Shi
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Kui Zheng
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
8
|
Rehman Z, Fahim A, Bhatti MF. Scouting the receptor-binding domain of SARS coronavirus 2: a comprehensive immunoinformatics inquisition. Future Virol 2021. [PMCID: PMC7899787 DOI: 10.2217/fvl-2020-0269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aim: December 2019 witnessed the emergence of a worldwide outbreak of a novel strain of coronavirus (CoV) termed SARS-CoV-2. Several preventive strategies are being developed, such as vaccines, to stop the spread of infection. Materials & methods: A comprehensive immunoinformatics approach was used to map conserved peptide sequences on the receptor binding domain of SARS-CoV-2 for their B-cell, T-helper & T-cytotoxic cell epitope profiles. Results & conclusion: The antigenic B-cell epitopes were LFRKSN and SYGFQPT. Among T-cell epitopes, CVADYSVLY and FTNVYADSF exhibited affinity for MHC class I, while YRLFRKSNL and VYAWNRKRI exhibited affinity for of MHC class II alleles. The overlapping epitope between B- and T-cells was YRLFRKSNL. The deployment of these epitopes in potential vaccine development against COVID-19 may help in slowing down the SARS-CoV-2 spread.
Collapse
Affiliation(s)
- Zaira Rehman
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Ammad Fahim
- Department of Multidisciplinary Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB),National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
| |
Collapse
|
9
|
Dai Y, Chen H, Zhuang S, Feng X, Fang Y, Tang H, Dai R, Tang L, Liu J, Ma T, Zhong G. Immunodominant regions prediction of nucleocapsid protein for SARS-CoV-2 early diagnosis: a bioinformatics and immunoinformatics study. Pathog Glob Health 2020; 114:463-470. [PMID: 33198594 PMCID: PMC7678408 DOI: 10.1080/20477724.2020.1838190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 is sweeping the world and posing serious health problems. Rapid and accurate detection along with timely isolation is the key to control the epidemic. Nucleic acid test and antibody-detection have been applied in the diagnosis of COVID-19, while both have their limitations. Comparatively, direct detection of viral antigens in clinical specimens is highly valuable for the early diagnosis of SARS-CoV-2. The nucleocapsid (N) protein is one of the predominantly expressed proteins with high immunogenicity during the early stages of infection. Here, we applied multiple bioinformatics servers to forecast the potential immunodominant regions derived from the N protein of SARS-CoV-2. Since the high homology of N protein between SARS-CoV-2 and SARS-CoV, we attempted to leverage existing SARS-CoV immunological studies to develop SARS-CoV-2 diagnostic antibodies. Finally, N229-269, N349-399, and N405-419 were predicted to be the potential immunodominant regions, which contain both predicted linear B-cell epitopes and murine MHC class II binding epitopes. These three regions exhibited good surface accessibility and hydrophilicity. All were forecasted to be non-allergen and non-toxic. The final construct was built based on the bioinformatics analysis, which could help to develop an antigen-capture system for the early diagnosis of SARS-CoV-2.
Collapse
Affiliation(s)
- Yufeng Dai
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Hongzhi Chen
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Metabolic Syndrome Research Center, and Department of Metabolism and Endocrinology, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Siqi Zhuang
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Xiaojing Feng
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Yiyuan Fang
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Haoneng Tang
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Ruchun Dai
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory for Metabolic Bone Diseases, Department of Metabolism and Endocrinology, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Lingli Tang
- Department of Laboratory Medicine, the Second Xiangya Hospital, Central South University , Changsha, Hunan, China
| | - Jun Liu
- Department of Radiology, The Second Xiangya Hospital, Central South University , Changsha, Hunan, 410011, China
| | - Tianmin Ma
- Asian International Collaboration, Waitemata District Health Board, New Zealand, Level 1 , Auckland, 15 Shea Terrace, 0622, New Zealand
| | - Guangming Zhong
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio , San Antonio,TX, 7703 Floyd Curl Drive, 78229, USA
| |
Collapse
|
10
|
Vallamkondu J, John A, Wani WY, Ramadevi SP, Jella KK, Reddy PH, Kandimalla R. SARS-CoV-2 pathophysiology and assessment of coronaviruses in CNS diseases with a focus on therapeutic targets. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165889. [PMID: 32603829 PMCID: PMC7320676 DOI: 10.1016/j.bbadis.2020.165889] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 02/06/2023]
Abstract
The novel Coronavirus disease of 2019 (nCOV-19) is a viral outbreak noted first in Wuhan, China. This disease is caused by Severe Acute Respiratory Syndrome (SARS) Coronavirus (CoV)-2. In the past, other members of the coronavirus family, such as SARS and Middle East Respiratory Syndrome (MERS), have made an impact in China and the Arabian peninsula respectively. Both SARS and COVID-19 share similar symptoms such as fever, cough, and difficulty in breathing that can become fatal in later stages. However, SARS and MERS infections were epidemic diseases constrained to limited regions. By March 2020 the SARS-CoV-2 had spread across the globe and on March 11th, 2020 the World Health Organization (WHO) declared COVID-19 as pandemic disease. In severe SARS-CoV-2 infection, many patients succumbed to pneumonia. Higher rates of deaths were seen in older patients who had co-morbidities such as diabetes mellitus, hypertension, cardiovascular disease (CVD), and dementia. In this review paper, we discuss the effect of SARS-CoV-2 on CNS diseases, such as Alzheimer's-like dementia, and diabetes mellitus. We also focus on the virus genome, pathophysiology, theranostics, and autophagy mechanisms. We will assess the multiorgan failure reported in advanced stages of SARS-CoV-2 infection. Our paper will provide mechanistic clues and therapeutic targets for physicians and investigators to combat COVID-19.
Collapse
Affiliation(s)
| | - Albin John
- Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Willayat Yousuf Wani
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States
| | | | | | - P Hemachandra Reddy
- Professor of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Internal Medicine, Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Ramesh Kandimalla
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, Telangana, India; Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India.
| |
Collapse
|
11
|
Prajapat M, Sarma P, Shekhar N, Avti P, Sinha S, Kaur H, Kumar S, Bhattacharyya A, Kumar H, Bansal S, Medhi B. Drug targets for corona virus: A systematic review. Indian J Pharmacol 2020; 52:56-65. [PMID: 32201449 PMCID: PMC7074424 DOI: 10.4103/ijp.ijp_115_20] [Citation(s) in RCA: 276] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
The 2019-novel coronavirus (nCoV) is a major source of disaster in the 21th century. However, the lack of specific drugs to prevent/treat an attack is a major need at this current point of time. In this regard, we conducted a systematic review to identify major druggable targets in coronavirus (CoV). We searched PubMed and RCSB database with keywords HCoV, NCoV, corona virus, SERS-CoV, MERS-CoV, 2019-nCoV, crystal structure, X-ray crystallography structure, NMR structure, target, and drug target till Feb 3, 2020. The search identified seven major targets (spike protein, envelop protein, membrane protein, protease, nucleocapsid protein, hemagglutinin esterase, and helicase) for which drug design can be considered. There are other 16 nonstructural proteins (NSPs), which can also be considered from the drug design perspective. The major structural proteins and NSPs may serve an important role from drug design perspectives. However, the occurrence of frequent recombination events is a major deterrent factor toward the development of CoV-specific vaccines/drugs.
Collapse
Affiliation(s)
- Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shweta Sinha
- Department of Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anusuya Bhattacharyya
- Departments of Ophthalmology, Government Medical College and Hospital, Chandigarh, India
| | - Harish Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Seema Bansal
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
12
|
Prajapat M, Sarma P, Shekhar N, Avti P, Sinha S, Kaur H, Kumar S, Bhattacharyya A, Kumar H, Bansal S, Medhi B. Drug targets for corona virus: A systematic review. Indian J Pharmacol 2020. [PMID: 32201449 DOI: 10.4103/ijp.ijp.115-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
The 2019-novel coronavirus (nCoV) is a major source of disaster in the 21th century. However, the lack of specific drugs to prevent/treat an attack is a major need at this current point of time. In this regard, we conducted a systematic review to identify major druggable targets in coronavirus (CoV). We searched PubMed and RCSB database with keywords HCoV, NCoV, corona virus, SERS-CoV, MERS-CoV, 2019-nCoV, crystal structure, X-ray crystallography structure, NMR structure, target, and drug target till Feb 3, 2020. The search identified seven major targets (spike protein, envelop protein, membrane protein, protease, nucleocapsid protein, hemagglutinin esterase, and helicase) for which drug design can be considered. There are other 16 nonstructural proteins (NSPs), which can also be considered from the drug design perspective. The major structural proteins and NSPs may serve an important role from drug design perspectives. However, the occurrence of frequent recombination events is a major deterrent factor toward the development of CoV-specific vaccines/drugs.
Collapse
Affiliation(s)
- Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shweta Sinha
- Department of Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anusuya Bhattacharyya
- Departments of Ophthalmology, Government Medical College and Hospital, Chandigarh, India
| | - Harish Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Seema Bansal
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
13
|
Liu WJ, Lan J, Liu K, Deng Y, Yao Y, Wu S, Chen H, Bao L, Zhang H, Zhao M, Wang Q, Han L, Chai Y, Qi J, Zhao J, Meng S, Qin C, Gao GF, Tan W. Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC. THE JOURNAL OF IMMUNOLOGY 2016; 198:873-882. [PMID: 27903740 DOI: 10.4049/jimmunol.1601542] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/06/2016] [Indexed: 12/20/2022]
Abstract
The coordinated recognition of virus-derived T cell epitopes and MHC molecules by T cells plays a pivotal role in cellular immunity-mediated virus clearance. It has been demonstrated that the conformation of MHC class I (MHC I) molecules can be adjusted by the presented peptide, which impacts T cell activation. However, it is still largely unknown whether the conformational shift of MHC I influences the protective effect of virus-specific T cells. In this study, utilizing the Middle East respiratory syndrome coronavirus-infected mouse model, we observed that through the unusual secondary anchor Ile5, a CD8+ T cell epitope drove the conformational fit of Trp73 on the α1 helix of murine MHC I H-2Kd In vitro renaturation and circular dichroism assays indicated that this shift of the structure did not influence the peptide/MHC I binding affinity. Nevertheless, the T cell recognition and the protective effect of the peptide diminished when we made an Ile to Ala mutation at position 5 of the original peptide. The molecular bases of the concordant recognition of T cell epitopes and host MHC-dependent protection were demonstrated through both crystal structure determination and tetramer staining using the peptide-MHC complex. Our results indicate a coordinated MHC I/peptide interaction mechanism and provide a beneficial reference for T cell-oriented vaccine development against emerging viruses such as Middle East respiratory syndrome coronavirus.
Collapse
Affiliation(s)
- William J Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jiaming Lan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang 050017, China
| | - Kefang Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yao Deng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanfeng Yao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Hong Chen
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lingling Bao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Haifeng Zhang
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; and
| | - Songdong Meng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - George F Gao
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjie Tan
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| |
Collapse
|
14
|
Liu WJ, Zhao M, Liu K, Xu K, Wong G, Tan W, Gao GF. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV. Antiviral Res 2016; 137:82-92. [PMID: 27840203 PMCID: PMC7113894 DOI: 10.1016/j.antiviral.2016.11.006] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/14/2022]
Abstract
Over 12 years have elapsed since severe acute respiratory syndrome (SARS) triggered the first global alert for coronavirus infections. Virus transmission in humans was quickly halted by public health measures and human infections of SARS coronavirus (SARS-CoV) have not been observed since. However, other coronaviruses still pose a continuous threat to human health, as exemplified by the recent emergence of Middle East respiratory syndrome (MERS) in humans. The work on SARS-CoV widens our knowledge on the epidemiology, pathophysiology and immunology of coronaviruses and may shed light on MERS coronavirus (MERS-CoV). It has been confirmed that T-cell immunity plays an important role in recovery from SARS-CoV infection. Herein, we summarize T-cell immunological studies of SARS-CoV and discuss the potential cross-reactivity of the SARS-CoV-specific immunity against MERS-CoV, which may provide useful recommendations for the development of broad-spectrum vaccines against coronavirus infections. T-cell epitopes identified throughout the SARS-CoV proteome may act as candidates for vaccine development. Both SARS-CoV and MERS-CoV-recovered donors have had long-lasting memory T-cell immunity. The structures of HLA/SARS-CoV-epitopes illuminate the molecular bases of cellular immunogenicity. Potential cross-T-cell immune reactivities of SARS-CoV and MERS-CoV benefit vaccine development.
Collapse
Affiliation(s)
- William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kefang Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gary Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
15
|
Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discov Today 2015; 21:562-72. [PMID: 26691874 PMCID: PMC7108309 DOI: 10.1016/j.drudis.2015.11.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Coronavirus nucleocapsid proteins are appealing drug targets against coronavirus-induced diseases. A variety of compounds targeting the coronavirus nucleocapsid protein have been developed. Many of these compounds show potential antiviral activity.
The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.
Collapse
|
16
|
Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An In Silico Approach Applied to Emerging Infectious Diseases. PLoS One 2015; 10:e0144475. [PMID: 26641892 PMCID: PMC4671582 DOI: 10.1371/journal.pone.0144475] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/18/2015] [Indexed: 12/12/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) with pandemic potential is a major worldwide threat to public health. However, vaccine development for this pathogen lags behind as immunity associated with protection is currently largely unknown. In this study, an immunoinformatics-driven genome-wide screening strategy of vaccine targets was performed to thoroughly screen the vital and effective dominant immunogens against MERS-CoV. Conservancy and population coverage analysis of the epitopes were done by the Immune Epitope Database. The results showed that the nucleocapsid (N) protein of MERS-CoV might be a better protective immunogen with high conservancy and potential eliciting both neutralizing antibodies and T-cell responses compared with spike (S) protein. Further, the B-cell, helper T-cell and cytotoxic T lymphocyte (CTL) epitopes were screened and mapped to the N protein. A total of 15 linear and 10 conformal B-cell epitopes that may induce protective neutralizing antibodies were obtained. Additionally, a total of 71 peptides with 9-mer core sequence were identified as helper T-cell epitopes, and 34 peptides were identified as CTL epitopes. Based on the maximum HLA binding alleles, top 10 helper T-cell epitopes and CTL epitopes that may elicit protective cellular immune responses against MERS-CoV were selected as MERS vaccine candidates. Population coverage analysis showed that the putative helper T-cell epitopes and CTL epitopes could cover the vast majority of the population in 15 geographic regions considered where vaccine would be employed. The B- and T-cell stimulation potentials of the screened epitopes is to be further validated for their efficient use as vaccines against MERS-CoV. Collectively, this study provides novel vaccine target candidates and may prompt further development of vaccines against MERS-CoV and other emerging infectious diseases.
Collapse
|
17
|
Liang FY, Lin LC, Ying TH, Yao CW, Tang TK, Chen YW, Hou MH. Immunoreactivity characterisation of the three structural regions of the human coronavirus OC43 nucleocapsid protein by Western blot: implications for the diagnosis of coronavirus infection. J Virol Methods 2012; 187:413-20. [PMID: 23174159 PMCID: PMC7112824 DOI: 10.1016/j.jviromet.2012.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 10/15/2012] [Accepted: 11/08/2012] [Indexed: 01/25/2023]
Abstract
Previous studies have reported that a prokaryotic-expressed recombinant nucleocapsid protein (NP) is a suitable reagent for the epidemiological screening of coronavirus infection. In this study, soluble recombinant human coronavirus OC43 (HCoV-OC43) NP was produced to examine the antigenicity of the HCoV-OC43 NP of betacoronavirus. Using the purified recombinant NP as an antigen, a polyclonal antibody from rabbit serum with specificity for HCoV-OC43 NP was generated; this antibody reacts specifically with HCoV-OC43 NP and does not cross-react with other human CoV NPs (including those of SARS-CoV and HCoV-229E) by Western blot. Sera from 26 young adults, 17 middle-aged and elderly patients with respiratory infection, and 15 cord blood samples were also tested. Strong reactivity to the NPs of HCoV-OC43 was observed in 96%, 82%, and 93% of the serum samples from the young adults, respiratory patients, and cord blood samples, respectively. To identify the immunoreactivities of the three structural regions of the NP that are recognised by the rabbit polyclonal antibody and human serum, the antigenicities of three protein fragments, including the N-terminal domain (aa 1-173), the central-linker region (aa 174-300), and the C-terminal domain (aa 301-448), were evaluated by Western blot. The rabbit polyclonal antibody demonstrated greater immunoreactivity to the central-linker region and the C-terminal domain than to the N-terminal domain. Three different patterns for the immunoreactivities of the three structural regions of HCoV-OC43 NP were observed in human serum, suggesting variability in the immune responses that occur during HCoV-OC43 infection in humans. The central-linker region of the NP appeared to be the most highly immunoreactive region for all three patterns observed. The goal of this study was to offer insight into the design of diagnostic tools for HCoV infection.
Collapse
Affiliation(s)
- Fang-Ying Liang
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | | | | | | | | | | | | |
Collapse
|
18
|
Qiu X, Hong C, Li Y, Bao W, Gao XM. Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus. Microbiol Immunol 2012; 56:554-61. [PMID: 22530918 PMCID: PMC7168421 DOI: 10.1111/j.1348-0421.2012.00467.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 12/02/2022]
Abstract
Fragment 450-650 of the spike (S) protein (S450-650) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains epitopes capable of being recognized by convalescent sera of SARS patients. Vaccination of mice with recombinant S450-650 (rS450-650) can induce Abs against SARS-CoV, although the titer is relatively low. In the present study, a fusion protein linking a fragment (residues 39-272) of murine calreticulin (CRT) to S450-650 in a prokaryotic expression system was created. Compared with target antigen alone, the recombinant fusion product (rS450-650-CRT) has much improved hydrophilicity and immunogenicity. The S450-650-specific IgG Abs of BALB/c mice subcutaneously immunized with rS450-650-CRT were in substantially higher titer (approximately fivefold more). Furthermore, the fusion protein, but not rS450-650 alone, was able to elicit S450-650-specific IgG responses in T cell deficient nude mice. Given that rCRT/39-272 can drive the maturation of bone-marrow-derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39-272 of CRT is an effective molecular adjuvant capable of enhancing target Ag-specific humoral responses in both a T cell-dependent and independent manner. Fusion protein rS450-650-CRT is a potential candidate vaccine against SARS-CoV infection.
Collapse
Affiliation(s)
- Xiang Qiu
- Department of Immunology, Peking University Health Science Center, Beijing, China
| | | | | | | | | |
Collapse
|
19
|
Wang S, Wu X, Pan T, Song W, Wang Y, Zhang F, Yuan Z. Viperin inhibits hepatitis C virus replication by interfering with binding of NS5A to host protein hVAP-33. J Gen Virol 2011; 93:83-92. [PMID: 21957124 DOI: 10.1099/vir.0.033860-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Viperin is a type-I and -II interferon-inducible intracytoplasmic protein that mediates antiviral activity against several viruses. A previous study has reported that viperin could limit hepatitis C virus (HCV) replication in vitro. However, the underlying mechanism remains elusive. In the present study, we found that overexpression of viperin could inhibit HCV replication in a dose-dependent manner in both the replicon and HCVcc systems. Furthermore, through co-immunoprecipitation and laser confocal microscopic analysis, viperin was found to interact with the host protein hVAP-33. Mutagenesis analysis demonstrated that the anti-HCV activity of viperin was located to its C terminus, which was required for the interaction with the C-terminal domain of hVAP-33. Competitive co-immunoprecipitation analysis showed that viperin could interact competitively with hVAP-33, and could therefore interfere with its interactions with HCV NS5A. In summary, these findings suggest a novel mechanism by which viperin inhibits HCV replication, possibly through binding to host protein hVAP-33 and interfering with its interaction with NS5A.
Collapse
Affiliation(s)
- Shanshan Wang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Xianfang Wu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Tingting Pan
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
| | - Wuhui Song
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
| | - Yaohui Wang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
| | - Fei Zhang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| |
Collapse
|
20
|
Genetic variation of the human α-2-Heremans-Schmid glycoprotein (AHSG) gene associated with the risk of SARS-CoV infection. PLoS One 2011; 6:e23730. [PMID: 21904596 PMCID: PMC3163911 DOI: 10.1371/journal.pone.0023730] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 07/26/2011] [Indexed: 12/18/2022] Open
Abstract
Genetic background may play an important role in the process of SARS-CoV
infection and SARS development. We found several proteins that could interact
with the nucleocapsid protein of the SARS coronavirus (SARS-CoV).
α-2-Heremans-Schmid Glycoprotein (AHSG), which is required for macrophage
deactivation by endogenous cations, is associated with inflammatory regulation.
Cytochrome P450 Family 3A (CYP4F3A) is an ω-oxidase that
inactivates Leukotriene B4 (LTB4) in human neutrophils and the liver. We
investigated the association between the polymorphisms of these two
inflammation-associated genes and SARS development. The linkage disequilibrium
(LD) maps of these two genes were built with Haploview using data on
CHB+JPT (version 2) from the HapMap. A total of ten tag SNPs were selected
and genotyped. In the Guangzhou cohort study, after adjusting for age and sex,
two AHSG SNPs and one CYP4F3 SNP were found to
be associated with SARS susceptibility: rs2248690 (adjusted odds ratio
[AOR] 2.42; 95% confidence interval [CI] 1.30-4.51);
rs4917 (AOR 1.84; 95% CI 1.02-3.34); and rs3794987 (AOR 2.01; 95%
CI 1.10–3.68). To further validate the association, the ten tag SNPs were
genotyped in the Beijing cohort. After adjusting for age and sex, only rs2248690
(AOR, 1.63; 95% CI, 1.30–2.04) was found to be associated with SARS
susceptibility. The combined analysis of the two studies confirmed tag SNP
rs2248690 in AHSG as a susceptibility variant (AOR 1.70;
95% CI 1.37–2.09). The statistical analysis of the rs2248690
genotype data among the patients and healthy controls in the HCW cohort, who
were all similarly exposed to the SARS virus, also supported the findings.
Further, the SNP rs2248690 affected the transcriptional activity of the
AHSG promoter and thus regulated the AHSG serum level.
Therefore, our study has demonstrated that the AA genotype of rs2268690, which
leads to a higher AHSG serum concentration, was significantly associated with
protection against SARS development.
Collapse
|
21
|
Rossi G, Cornaro C, Battilani M, Pocacqua V, Paltrinieri S. Production of IFN-γ in feline whole blood after incubation with potential T-cell epitopes of the nucleocapsid protein of feline coronavirus. Vet Microbiol 2011; 150:248-56. [PMID: 21376481 PMCID: PMC7117359 DOI: 10.1016/j.vetmic.2011.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 12/20/2010] [Accepted: 02/08/2011] [Indexed: 11/30/2022]
Abstract
Interferon gamma (IFN-γ) plays an important role in cell mediated responses against mutated feline coronavirus strains (FCoV) involved in the pathogenesis of feline infectious peritonitis (FIP). The aim of this study was to establish a combined in silico and in vitro approach to assess feline leukocyte production of IFN-γ in response to selected peptides of the nucleocapside protein (N) of FCoVs. To this aim, we designed, through a bioinformatic approach, 8 potentially immunogenic peptides from the protein N corresponding to sequences of residues 14, 182, 198 detected only in FCoVs from FIP cats (virulent strains), only in FCoVs from healthy cats (avirulent strains) and both in FIP and in healthy cats (mixed strains). The peptides or a sham solution were incubated with whole blood from 16 cats (7 healthy and 9 with chronic diseases other than FIP) and IFN-γ concentration was measured on plasma using an ELISA system. RT-PCR expression of IFN-γ mRNA was also evaluated after incubation of the peptides or a sham solution with whole blood from 4 clinically healthy cats. The mean plasma concentration of IFN-γ in samples incubated with peptides decreased and the expression of IFN-γmRNA did not change compared with the sham solution, except for some cats with chronic diseases (which probably have a “pre-activated” immune response). These cats responded to “avirulent” or “mixed” peptides by increasing the concentration of IFN-γ and the expression of IFN-γ mRNA. The combined approach employed in this study allowed us to identify potentially immunogenic peptides of FCoV N protein that can modulate the production of IFN-γ especially in cats with a “pre-activated” cell mediated response.
Collapse
Affiliation(s)
- G Rossi
- Department of Veterinary Pathology, Hygiene and Public Health, Unit of Veterinary General Pathology and Parasitology, University of Milan, Via Celoria 10, 20133 Milan, Italy
| | | | | | | | | |
Collapse
|
22
|
Satoh R, Kobayashi H, Takano T, Motokawa K, Kusuhara H, Hohdatsu T. Characterization of T helper (Th)1- and Th2-type immune responses caused by baculovirus-expressed protein derived from the S2 domain of feline infectious peritonitis virus, and exploration of the Th1 and Th2 epitopes in a mouse model. Microbiol Immunol 2011; 54:726-33. [PMID: 21091984 PMCID: PMC7168408 DOI: 10.1111/j.1348-0421.2010.00275.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Feline infectious peritonitis virus (FIPV) may cause a lethal infection in cats. Antibody‐dependent enhancement (ADE) of FIPV infection has been recognized, and cellular immunity is considered to play an important role in preventing the onset of feline infectious peritonitis. In the present study, whether or not the T helper (Th)1 epitope was present in the spike (S)2 domain was investigated, the ADE epitope being thought to be absent from this domain. Three kinds of protein derived from the C‐terminal S2 domain of S protein of the FIPV KU‐2 strain were developed using a baculovirus expression system. These expressed proteins were the pre‐coil region which is the N‐terminal side of the putative fusion protein (FP), the region from FP to the heptad repeat (HR)2 (FP‐HR2) region, and the inter‐helical region which is sandwiched between HR1 and HR2. The ability of three baculovirus‐expressed proteins to induce Th1‐ and Th2‐type immune responses was investigated in a mouse model. It was shown that FP‐HR2 protein induced marked Th1‐ and Th2‐type immune responses. Furthermore, 30 peptides derived from the FP‐HR2 region were synthesized. Five and 16 peptides which included the Th1 and Th2 epitopes, respectively, were identified. Of these, four peptides which included both Th1 and Th2 epitopes were identified. These findings suggest that the identification of Th1 epitopes in the S2 domain of FIPV has important implications in the cat.
Collapse
|
23
|
Satoh R, Furukawa T, Kotake M, Takano T, Motokawa K, Gemma T, Watanabe R, Arai S, Hohdatsu T. Screening and identification of T helper 1 and linear immunodominant antibody-binding epitopes in the spike 2 domain and the nucleocapsid protein of feline infectious peritonitis virus. Vaccine 2011; 29:1791-800. [PMID: 21216312 PMCID: PMC7115570 DOI: 10.1016/j.vaccine.2010.12.106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/24/2010] [Accepted: 12/22/2010] [Indexed: 01/12/2023]
Abstract
The antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection has been recognized in experimentally infected cats, and cellular immunity is considered to play an important role in preventing the onset of feline infectious peritonitis (FIP). In the present study, we synthesized eighty-one kinds of peptides derived from the spike (S)2 domain of type I FIPV KU-2 strain, the S2 domain of type II FIPV 79-1146 strain, and the nucleocapcid (N) protein of FIPV KU-2 strain. To detect the T helper (Th)1 epitope, peripheral blood mononuclear cells (PBMCs) obtained from FIPV-infected cats were cultured with each peptide, and Th1-type immune responses were measured using feline interferon (fIFN)-γ production as an index. To detect the linear immunodominant antibody-binding epitope, we investigated the reactivity of plasma collected from FIPV-infected cats against each peptide by ELISA. Four and 2 peptides containing Th1 epitopes were identified in the heptad repeat (HR)1 and inter-helical (IH) regions of the S2 domain of type I FIPV, respectively, and these were located on the N-terminal side of the regions. In the S2 domain of type II FIPV, 2, 3, and 2 peptides containing Th1 epitopes were identified in the HR1, IH, and HR2 regions, respectively, and these were mainly located on the C-terminal side of the regions. In the S2 domain of type I FIPV, 3 and 7 peptides containing linear immunodominant antibody-binding epitopes were identified in the IH and HR2 regions, respectively. In the S2 domain of type II FIPV, 4 peptides containing linear immunodominant antibody-binding epitopes were identified in the HR2 region. The Th1 epitopes in the S2 domain of type I and II FIPV were located in different regions, but the linear immunodominant antibody-binding epitopes were mostly located in the HR2 region. Eight peptides containing Th1 epitopes were identified in N protein, and 3 peptides derived from residues 81 to 100 and 137 to 164 showed strong inductivity of fIFN-γ production in PBMCs isolated from type I FIPV- and type II FIPV-infected non-FIP cats. In N protein, 4 peptides containing linear immunodominant antibody-binding epitopes were identified, and 2 peptides derived from residues 345 to 372 showed strong reactivity with plasma of type I FIPV- and type II FIPV-infected cats. The Th1 and linear immunodominant antibody-binding epitopes were located at different positions in both the S2 domain and N protein. Our results may provide important information for the development of peptide-based vaccine against FIPV infection.
Collapse
Affiliation(s)
- Ryoichi Satoh
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Ahn I, Jeong BJ, Son HS. Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse. Exp Mol Med 2010; 41:746-56. [PMID: 19561398 PMCID: PMC2772977 DOI: 10.3858/emm.2009.41.10.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.
Collapse
Affiliation(s)
- Insung Ahn
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejon 305-806, Korea
| | | | | |
Collapse
|
25
|
Netland J, DeDiego ML, Zhao J, Fett C, Álvarez E, Nieto-Torres JL, Enjuanes L, Perlman S. Immunization with an attenuated severe acute respiratory syndrome coronavirus deleted in E protein protects against lethal respiratory disease. Virology 2010; 399:120-128. [PMID: 20110095 PMCID: PMC2830353 DOI: 10.1016/j.virol.2010.01.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/19/2009] [Accepted: 01/05/2010] [Indexed: 01/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) caused substantial morbidity and mortality in 2002–2003. Deletion of the envelope (E) protein modestly diminished virus growth in tissue culture but abrogated virulence in animals. Here, we show that immunization with rSARS-CoV-ΔE or SARS-CoV-Δ[E,6-9b] (deleted in accessory proteins (6, 7a, 7b, 8a, 8b, 9b) in addition to E) nearly completely protected BALB/c mice from fatal respiratory disease caused by mouse-adapted SARS-CoV and partly protected hACE2 Tg mice from lethal disease. hACE2 Tg mice, which express the human SARS-CoV receptor, are extremely susceptible to infection. We also show that rSARS-CoV-ΔE and rSARS-CoV-Δ[E,6-9b] induced anti-virus T cell and antibody responses. Further, the E-deleted viruses were stable after 16 blind passages through tissue culture cells, with only a single mutation in the surface glycoprotein detected. The passaged virus remained avirulent in mice. These results suggest that rSARS-CoV-ΔE is an efficacious vaccine candidate that might be useful if SARS recurred.
Collapse
Affiliation(s)
- Jason Netland
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242
| | - Marta L DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnolgia (CSIC), Campus Universidad Autonoma, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Jincun Zhao
- Department of Microbiology, University of Iowa, Iowa City, IA 52242
| | - Craig Fett
- Department of Microbiology, University of Iowa, Iowa City, IA 52242
| | - Enrique Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnolgia (CSIC), Campus Universidad Autonoma, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José L Nieto-Torres
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnolgia (CSIC), Campus Universidad Autonoma, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnolgia (CSIC), Campus Universidad Autonoma, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Stanley Perlman
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242; Department of Microbiology, University of Iowa, Iowa City, IA 52242.
| |
Collapse
|
26
|
Yasui F, Kai C, Saito K, Inoue S, Yoneda M, Morita K, Mizuno K, Kohara M. Analysis of the mechanism by which BALB/c mice having prior immunization with nucleocapsid protein of SARS-CoV develop severe pneumonia after SARS-CoV infection. ACTA ACUST UNITED AC 2010; 2:44-50. [PMID: 32288911 PMCID: PMC7128161 DOI: 10.1016/j.provac.2010.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The precise mechanism of severe acute respiratory syndrome (SARS), which is caused by SARS-associated coronavirus (SARS-CoV), is still unclear. We generated recombinant vaccinia virus (rVV) LC16m8 strain which simultaneously expresses four structural proteins of SARS-CoV, including nucleocapsid (N), membrane (M), envelop (E), spike (S) proteins (rVV-NMES) and reported that old BALB/c mice having prior immunization with rVV-NMES develop severe pneumonia similar to those of control mice though rVV-NMES-immunized mice showed lower pulmonary viral titer than in the control mice. Furthermore, we determined which SARS-CoV structural protein for the prior rVV-immunization is responsible for the severe pneumonia after the SARS-CoV infection as observed in the rVV-NMES-immunized mice. Old BALB/c mice were inoculated intradermally with rVV that expressed each structural proteins of SARS-CoV (rVV-N, -M, -E, or -S) with or without rVV-S and then infected intranasally with SARS-CoV more than 4 weeks later. At 9 days after SARS-CoV infection, the rVV-N-immunized mice show more severe pneumonia than in other groups. Furthermore, significant up-regulation of Th1 (IL-2)- and Th2 (IL-4 and IL-5)-bias cytokines and down-regulation of anti-inflammatory cytokine (IL-10 and TGF-β) were observed in rVV-N-immunized mice, resulting in the intensive infiltration of immunocompetent cells into the lung. In contrast, rVV-S-immunized mice showed only low pulmonary viral tier and slight pneumonia. However, the mice having co-immunization with both rVV-N and rVV-S showed severe pneumonia though their pulmonary viral titer was low. These results suggest that an excessive host immune response against the N protein of SARS-CoV is involved in severe pneumonia caused by SARS-CoV infection. These findings increase our understanding of the pathogenesis of SARS.
Collapse
Affiliation(s)
- Fumihiko Yasui
- Dep. Micobiol. & Cell Biol., Tokyo Metro. Inst. Med. Sci
| | - Chieko Kai
- Lab. Animal Res. Center, The Inst. Med. Sci., Univ. of Tokyo
| | - Kousuke Saito
- Dep. Micobiol. & Cell Biol., Tokyo Metro. Inst. Med. Sci
| | - Shingo Inoue
- Dep. of Virol., Inst. of Tropic. Med., Nagasaki Univ
| | - Misako Yoneda
- Lab. Animal Res. Center, The Inst. Med. Sci., Univ. of Tokyo
| | | | | | | |
Collapse
|
27
|
Yang K, Sun K, Srinivasan KN, Salmon J, Marques ET, Xu J, August JT. Immune responses to T-cell epitopes of SARS CoV-N protein are enhanced by N immunization with a chimera of lysosome-associated membrane protein. Gene Ther 2009; 16:1353-62. [PMID: 19727132 PMCID: PMC7091638 DOI: 10.1038/gt.2009.92] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 05/11/2009] [Accepted: 06/05/2009] [Indexed: 12/30/2022]
Abstract
In our previous study by Gupta et al, dominant T-cell epitopes of SARS CoV-N(N) protein were predicted by software. The spectrum of interferon (IFN)-gamma responses of Balb/c mice immunized against two different forms of SARS CoV-N plasmid was then analyzed. A cluster of dominant T-cell epitopes of SARS CoV-N protein was found in the N-terminus (amino acids 76-114). On the basis of this study, four different plasmids were constructed: (i) DNA encoding the unmodified N (p-N) or N(70-122) (p-N(70-122)) as an endogenous cytoplasmic protein or (ii) DNA encoding a lysosome-associated membrane protein (LAMP) chimera with N (p-LAMP/N) or N(70-122) (p-LAMP/N(70-122)). The immune responses of mice to these four constructs were evaluated. The results showed marked differences in the responses of the immunized mice. A single priming immunization with the p-LAMP/N construct was sufficient to elicit an antibody response. Enzyme-linked immunospot (ELISpot) assay indicated that p-LAMP/N(70-122) and p-LAMP/N plasmids both elicited a greater IFN-gamma response than p-N. p-N and p-N(70-122) constructs induced low or undetectable levels of cytokine secretion. We also found that the p-LAMP/N(70-122) construct promoted a long-lasting T-cell memory response without an additional boost 6 months after three immunizations. These findings show that DNA vaccines, even epitope-based DNA vaccines using LAMP as chimera, can elicit both humoral and cellular immune responses.
Collapse
Affiliation(s)
- K Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi Province, PR China,
| | - K Sun
- Division of Biomedical Sciences, Johns Hopkins in Singapore, Singapore
| | - K N Srinivasan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD USA
- Product Evaluation and Registration Division, Centre for Drug Administration, Health Sciences Authority, Singapore
| | - J Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - E T Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD USA
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - J Xu
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi Province, PR China,
| | - J T August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| |
Collapse
|
28
|
The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential. MOLECULAR BIOLOGY OF THE SARS-CORONAVIRUS 2009. [PMCID: PMC7176212 DOI: 10.1007/978-3-642-03683-5_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As in other coronaviruses, the nucleocapsid protein is one of the core components of the SARS coronavirus (CoV). It oligomerizes to form a closed capsule, inside which the genomic RNA is securely stored thus providing the SARS-CoV genome with its first line of defense from the harsh conditions of the host environment and aiding in replication and propagation of the virus. In addition to this function, several reports have suggested that the SARS-CoV nucleocapsid protein modulates various host cellular processes, so as to make the internal milieu of the host more conducive for survival of the virus. This article will analyze and discuss the available literature regarding these different properties of the nucleocapsid protein. Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection.
Collapse
|
29
|
Zheng N, Xia R, Yang C, Yin B, Li Y, Duan C, Liang L, Guo H, Xie Q. Boosted expression of the SARS-CoV nucleocapsid protein in tobacco and its immunogenicity in mice. Vaccine 2009; 27:5001-7. [PMID: 19523911 PMCID: PMC7115566 DOI: 10.1016/j.vaccine.2009.05.073] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 05/20/2009] [Accepted: 05/26/2009] [Indexed: 12/18/2022]
Abstract
Vaccines produced in plant systems are safe and economical; however, the extensive application of plant-based vaccines is mainly hindered by low expression levels of heterologous proteins in plant systems. Here, we demonstrated that the post-transcriptional gene silencing suppressor p19 protein from tomato bushy stunt virus substantially enhanced the transient expression of recombinant SARS-CoV nucleocapsid (rN) protein in Nicotiana benthamiana. The rN protein in the agrobacteria-infiltrated plant leaf accumulated up to a concentration of 79 microg per g fresh leaf weight at 3 days post infiltration. BALB/c mice were intraperitoneally vaccinated with pre-treated plant extract emulsified in Freund's adjuvant. The rN protein-specific IgG in the mouse sera attained a titer about 1:1,800 following three doses of immunization, which suggested effective B-cell maturation and differentiation in mice. Antibodies of the subclasses IgG1 and IgG2a were abundantly present in the mouse sera. During vaccination of rN protein, the expression of IFN-gamma and IL-10 was evidently up-regulated in splenocytes at different time points, while the expression of IL-2 and IL-4 was not. Up to now, this is the first study that plant-expressed recombinant SARS-CoV N protein can induce strong humoral and cellular responses in mice.
Collapse
MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Immunologic/pharmacology
- Animals
- Antibodies, Viral/blood
- Coronavirus Nucleocapsid Proteins
- Female
- Freund's Adjuvant/administration & dosage
- Freund's Adjuvant/pharmacology
- Gene Silencing
- Humans
- Immunoglobulin G/blood
- Injections, Intraperitoneal
- Interferon-gamma/metabolism
- Interleukin-10/metabolism
- Leukocytes, Mononuclear/immunology
- Mice
- Mice, Inbred BALB C
- Nucleocapsid Proteins/genetics
- Nucleocapsid Proteins/immunology
- Nucleocapsid Proteins/isolation & purification
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/immunology
- Spleen/immunology
- Nicotiana/genetics
- Nicotiana/metabolism
- Tombusvirus/genetics
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vaccines, Subunit/isolation & purification
Collapse
Affiliation(s)
- Nuoyan Zheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
- State Key Laboratory for Biocontrol, Sun Yat-sen (Zhongshan) University, 135 Xingang Road W, Guangzhou 510275, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
| | - Cuiping Yang
- State Key Laboratory for Biocontrol, Sun Yat-sen (Zhongshan) University, 135 Xingang Road W, Guangzhou 510275, China
| | - Bojiao Yin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
- State Key Laboratory for Biocontrol, Sun Yat-sen (Zhongshan) University, 135 Xingang Road W, Guangzhou 510275, China
| | - Yin Li
- State Key Laboratory for Biocontrol, Sun Yat-sen (Zhongshan) University, 135 Xingang Road W, Guangzhou 510275, China
| | - Chengguo Duan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Liming Liang
- State Key Laboratory for Biocontrol, Sun Yat-sen (Zhongshan) University, 135 Xingang Road W, Guangzhou 510275, China
| | - Huishan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
| |
Collapse
|
30
|
Yasui F, Kai C, Kitabatake M, Inoue S, Yoneda M, Yokochi S, Kase R, Sekiguchi S, Morita K, Hishima T, Suzuki H, Karamatsu K, Yasutomi Y, Shida H, Kidokoro M, Mizuno K, Matsushima K, Kohara M. Prior immunization with severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) nucleocapsid protein causes severe pneumonia in mice infected with SARS-CoV. THE JOURNAL OF IMMUNOLOGY 2009; 181:6337-48. [PMID: 18941225 DOI: 10.4049/jimmunol.181.9.6337] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The details of the mechanism by which severe acute respiratory syndrome-associated coronavirus (SARS-CoV) causes severe pneumonia are unclear. We investigated the immune responses and pathologies of SARS-CoV-infected BALB/c mice that were immunized intradermally with recombinant vaccinia virus (VV) that expressed either the SARS-CoV spike (S) protein (LC16m8rVV-S) or simultaneously all the structural proteins, including the nucleocapsid (N), membrane (M), envelope (E), and S proteins (LC16m8rVV-NMES) 7-8 wk before intranasal SARS-CoV infection. The LC16m8rVV-NMES-immunized group exhibited as severe pneumonia as the control groups, although LC16m8rVV-NMES significantly decreased the pulmonary SARS-CoV titer to the same extent as LC16m8rVV-S. To identify the cause of the exacerbated pneumonia, BALB/c mice were immunized with recombinant VV that expressed the individual structural proteins of SARS-CoV (LC16mOrVV-N, -M, -E, -S) with or without LC16mOrVV-S (i.e., LC16mOrVV-N, LC16mOrVV-M, LC16mOrVV-E, or LC16mOrVV-S alone or LC16mOrVV-N + LC16mOrVV-S, LC16mOrVV-M + LC16mOrVV-S, or LC16mOrVV-E + LC16mOrVV-S), and infected with SARS-CoV more than 4 wk later. Both LC16mOrVV-N-immunized mice and LC16mOrVV-N + LC16mOrVV-S-immunized mice exhibited severe pneumonia. Furthermore, LC16mOrVV-N-immunized mice upon infection exhibited significant up-regulation of both Th1 (IFN-gamma, IL-2) and Th2 (IL-4, IL-5) cytokines and down-regulation of anti-inflammatory cytokines (IL-10, TGF-beta), resulting in robust infiltration of neutrophils, eosinophils, and lymphocytes into the lung, as well as thickening of the alveolar epithelium. These results suggest that an excessive host immune response against the nucleocapsid protein of SARS-CoV is involved in severe pneumonia caused by SARS-CoV infection. These findings increase our understanding of the pathogenesis of SARS.
Collapse
Affiliation(s)
- Fumihiko Yasui
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Mark J, Li X, Cyr T, Fournier S, Jaentschke B, Hefford MA. SARS coronavirus: unusual lability of the nucleocapsid protein. Biochem Biophys Res Commun 2008; 377:429-433. [PMID: 18926799 PMCID: PMC7092863 DOI: 10.1016/j.bbrc.2008.09.153] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 09/30/2008] [Indexed: 01/30/2023]
Abstract
The severe acute respiratory syndrome (SARS) is a contagious disease that killed hundreds and sickened thousands of people worldwide between November 2002 and July 2003. The nucleocapsid (N) protein of the coronavirus responsible for this disease plays a critical role in viral assembly and maturation and is of particular interest because of its potential as an antiviral target or vaccine candidate. Refolding of SARS N-protein during production and purification showed the presence of two additional protein bands by SDS-PAGE. Mass spectroscopy (MALDI, SELDI, and LC/MS) confirmed that the bands are proteolytic products of N-protein and the cleavage sites are four SR motifs in the serine-arginine-rich region-sites not suggestive of any known protease. Furthermore, results of subsequent testing for contaminating protease(s) were negative: cleavage appears to be due to inherent instability and/or autolysis. The importance of N-protein proteolysis to viral life cycle and thus to possible treatment directions are discussed.
Collapse
Affiliation(s)
- John Mark
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Xuguang Li
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Terry Cyr
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Sylvie Fournier
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Bozena Jaentschke
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2
| | - Mary Alice Hefford
- Centre for Biologics Research, Biologics and Genetic Therapies Directorate, Health Canada, 251 Sir Frederick Banting Driveway, AL:2201E, Ottawa, Ont., Canada K1A 0L2.
| |
Collapse
|
32
|
Yang J, James E, Roti M, Huston L, Gebe JA, Kwok WW. Searching immunodominant epitopes prior to epidemic: HLA class II-restricted SARS-CoV spike protein epitopes in unexposed individuals. Int Immunol 2008; 21:63-71. [PMID: 19050106 PMCID: PMC2638843 DOI: 10.1093/intimm/dxn124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Identification of dominant T cell epitopes within newly emerging and re-emerging infectious organisms is valuable in understanding pathogenic immune responses and potential vaccine designs. However, difficulties in obtaining samples from patients or convalescent subjects have hampered research in this direction. We demonstrated a strategy, tetramer-guided epitope mapping, that specific CD4+ T cell epitopes can be identified by using PBMC from subjects that have not been exposed to the infectious organism. Sixteen HLA-DR0401- and 14 HLA-DR0701-restricted epitopes within spike protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) were identified. Among these, spike protein residues 159-171, 166-178, 449-461 and 1083-1097 were identified to contain naturally processed immunodominant epitopes based on strong in vitro T cell responses of PBMC (as assayed by tetramer staining) to intact spike protein stimulation. These immunodominant epitopes were confirmed in vivo in HLA-DR0401 transgenic mice by immunizing with spike protein. Furthermore, the epitope-specific T cells from naive donors secreted IFN-gamma and IL-13 upon re-stimulation with corresponding tetramers. Our study demonstrates a strategy to determine potential immunodominant epitopes for emerging infectious pathogens prior to their epidemic circulation.
Collapse
Affiliation(s)
- Junbao Yang
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | | | | | | | | | | |
Collapse
|
33
|
Development of an enzyme-linked immunosorbent assay-based test with a cocktail of nucleocapsid and spike proteins for detection of severe acute respiratory syndrome-associated coronavirus-specific antibody. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2008; 16:241-5. [PMID: 19038782 DOI: 10.1128/cvi.00252-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A new enzyme-linked immunosorbent assay (ELISA)-based immunoglobulin G (IgG)-plus-IgM antibody detection test for severe acute respiratory syndrome (SARS) has been developed by using a cocktail of four recombinant polypeptides as the antigen. These recombinant fragments were designed as parts of two different structural proteins from SARS-associated coronavirus (SARS-CoV). One recombinant polypeptide, S251-683, was designed as part of the spike glycoprotein, and the other three polypeptides comprised almost the whole nucleocapsid protein, avoiding the last 25 C-terminal amino acids. Immunization with a cocktail of these four polypeptides yielded a specific polyclonal antibody that is able to recognize SARS-CoV-infected cells by an immunofluorescence assay. This polypeptide cocktail was also used to set up an ELISA-based IgG-plus-IgM antibody detection test, which showed 99% specificity and 90% sensitivity upon evaluation using sera from 100 healthy negative controls and 20 SARS patients. Separate immunoreactivity assays with each recombinant polypeptide demonstrated that a combination of N and S protein fragments was more suitable than the individual peptides for developing a serological assay for SARS-CoV.
Collapse
|
34
|
Li CKF, Wu H, Yan H, Ma S, Wang L, Zhang M, Tang X, Temperton NJ, Weiss RA, Brenchley JM, Douek DC, Mongkolsapaya J, Tran BH, Lin CLS, Screaton GR, Hou JL, McMichael AJ, Xu XN. T cell responses to whole SARS coronavirus in humans. THE JOURNAL OF IMMUNOLOGY 2008; 181:5490-500. [PMID: 18832706 DOI: 10.4049/jimmunol.181.8.5490] [Citation(s) in RCA: 376] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Effective vaccines should confer long-term protection against future outbreaks of severe acute respiratory syndrome (SARS) caused by a novel zoonotic coronavirus (SARS-CoV) with unknown animal reservoirs. We conducted a cohort study examining multiple parameters of immune responses to SARS-CoV infection, aiming to identify the immune correlates of protection. We used a matrix of overlapping peptides spanning whole SARS-CoV proteome to determine T cell responses from 128 SARS convalescent samples by ex vivo IFN-gamma ELISPOT assays. Approximately 50% of convalescent SARS patients were positive for T cell responses, and 90% possessed strongly neutralizing Abs. Fifty-five novel T cell epitopes were identified, with spike protein dominating total T cell responses. CD8(+) T cell responses were more frequent and of a greater magnitude than CD4(+) T cell responses (p < 0.001). Polychromatic cytometry analysis indicated that the virus-specific T cells from the severe group tended to be a central memory phenotype (CD27(+)/CD45RO(+)) with a significantly higher frequency of polyfunctional CD4(+) T cells producing IFN-gamma, TNF-alpha, and IL-2, and CD8(+) T cells producing IFN-gamma, TNF-alpha, and CD107a (degranulation), as compared with the mild-moderate group. Strong T cell responses correlated significantly (p < 0.05) with higher neutralizing Ab. The serum cytokine profile during acute infection indicated a significant elevation of innate immune responses. Increased Th2 cytokines were observed in patients with fatal infection. Our study provides a roadmap for the immunogenicity of SARS-CoV and types of immune responses that may be responsible for the virus clearance, and should serve as a benchmark for SARS-CoV vaccine design and evaluation.
Collapse
Affiliation(s)
- Chris Ka-fai Li
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Maciel M, Kellathur SN, Chikhlikar P, Dhalia R, Sidney J, Sette A, August TJ, Marques ET. Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model. Virology 2008; 378:105-17. [PMID: 18579176 PMCID: PMC2615555 DOI: 10.1016/j.virol.2008.04.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/07/2008] [Accepted: 04/30/2008] [Indexed: 01/19/2023]
Abstract
Immunomics research uses in silico epitope prediction, as well as in vivo and in vitro approaches. We inoculated BALB/c (H2d) mice with 17DD yellow fever vaccine to investigate the correlations between approaches used for epitope discovery: ELISPOT assays, binding assays, and prediction software. Our results showed a good agreement between ELISPOT and binding assays, which seemed to correlate with the protein immunogenicity. PREDBALB/c prediction software partially agreed with the ELISPOT and binding assay results, but presented low specificity. The use of prediction software to exclude peptides containing no epitopes, followed by high throughput screening of the remaining peptides by ELISPOT, and the use of MHC-biding assays to characterize the MHC restrictions demonstrated to be an efficient strategy. The results allowed the characterization of 2 MHC class I and 17 class II epitopes in the envelope protein of the YF virus in BALB/c (H2d) mice.
Collapse
Affiliation(s)
- Milton Maciel
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Srinivasan N. Kellathur
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA,Johns Hopkins Singapore, Singapore
| | - Pryia Chikhlikar
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Rafael Dhalia
- Oswaldo Cruz Foundation (FIOCRUZ), Instituto Aggeu Magalhaes, Recife, Brazil
| | | | | | - Thomas J. August
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Ernesto T.A. Marques
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA,Johns Hopkins, School of Medicine, Department of Infectious Diseases, Baltimore, USA,Oswaldo Cruz Foundation (FIOCRUZ), Instituto Aggeu Magalhaes, Recife, Brazil,Corresponding author. Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| |
Collapse
|
36
|
Surjit M, Lal SK. The SARS-CoV nucleocapsid protein: a protein with multifarious activities. INFECTION GENETICS AND EVOLUTION 2007; 8:397-405. [PMID: 17881296 PMCID: PMC7106238 DOI: 10.1016/j.meegid.2007.07.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2007] [Revised: 07/10/2007] [Accepted: 07/11/2007] [Indexed: 12/16/2022]
Abstract
Ever since the discovery of SARS-CoV in the year 2003, numerous researchers around the world have been working relentlessly to understand the biology of this virus. As in other coronaviruses, nucleocapsid (N) is one of the most crucial structural components of the SARS-CoV. Hence major attention has been focused on characterization of this protein. Independent studies conducted by several laboratories have elucidated significant insight into the primary function of this protein, which is to encapsidate the viral genome. In addition, many reports also suggest that this protein interferes with different cellular pathways, thus implying it to be a key regulatory component of the virus too. In the first part of this review, we will discuss these different properties of the N-protein in a consolidated manner. Further, this protein has also been proposed to be an efficient diagnostic tool and a candidate vaccine against the SARS-CoV. Hence, towards the end of this article, we will discuss some recent progress regarding the possible clinically relevant use of the N-protein.
Collapse
Affiliation(s)
| | - Sunil K. Lal
- Corresponding author at: Virology Group, ICGEB, P.O. Box 10504, Aruna Asaf Ali Road, New Delhi 110067, India. Tel.: +91 9818522900.
| |
Collapse
|
37
|
Richards KA, Chaves FA, Krafcik FR, Topham DJ, Lazarski CA, Sant AJ. Direct ex vivo analyses of HLA-DR1 transgenic mice reveal an exceptionally broad pattern of immunodominance in the primary HLA-DR1-restricted CD4 T-cell response to influenza virus hemagglutinin. J Virol 2007; 81:7608-19. [PMID: 17507491 PMCID: PMC1933370 DOI: 10.1128/jvi.02834-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The recent threat of an avian influenza pandemic has generated significant interest in enhancing our understanding of the events that dictate protective immunity to influenza and in generating vaccines that can induce heterosubtypic immunity. Although antigen-specific CD4 T cells are known to play a key role in protective immunity to influenza through the provision of help to B cells and CD8 T cells, little is known about the specificity and diversity of CD4 T cells elicited after infection, particularly those elicited in humans. In this study, we used HLA-DR transgenic mice to directly and comprehensively identify the specificities of hemagglutinin (HA)-specific CD4 T cells restricted to a human class II molecule that were elicited following intranasal infection with a strain of influenza virus that has been endemic in U.S. human populations for the last decade. Our results reveal a surprising degree of diversity among influenza virus-specific CD4 T cells. As many as 30 different peptides, spanning the entire HA protein, were recognized by CD4 T cells, including epitopes genetically conserved among H1, H2, and H5 influenza A viruses. We also compared three widely used major histocompatibility class II algorithms to predict HLA-DR binding peptides and found these as yet inadequate for identifying influenza virus-derived epitopes. The results of these studies offer key insights into the spectrum of peptides recognized by HLA-DR-restricted CD4 T cells that may be the focus of immune responses to infection or to experimental or clinical vaccines in humans.
Collapse
Affiliation(s)
- Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | | | | | | | | | | |
Collapse
|