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Morte-Romea E, Pesini C, Pellejero-Sagastizábal G, Letona-Giménez S, Martínez-Lostao L, Aranda SL, Toyas C, Redrado S, Dolader-Ballesteros E, Arias M, Galvez EM, Sanz-Pamplona R, Pardo J, Paño-Pardo JR, Ramírez-Labrada A. CAR Immunotherapy for the treatment of infectious diseases: a systematic review. Front Immunol 2024; 15:1289303. [PMID: 38352878 PMCID: PMC10861799 DOI: 10.3389/fimmu.2024.1289303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Immunotherapy treatments aim to modulate the host's immune response to either mitigate it in inflammatory/autoimmune disease or enhance it against infection or cancer. Among different immunotherapies reaching clinical application during the last years, chimeric antigen receptor (CAR) immunotherapy has emerged as an effective treatment for cancer where different CAR T cells have already been approved. Yet their use against infectious diseases is an area still relatively poorly explored, albeit with tremendous potential for research and clinical application. Infectious diseases represent a global health challenge, with the escalating threat of antimicrobial resistance underscoring the need for alternative therapeutic approaches. This review aims to systematically evaluate the current applications of CAR immunotherapy in infectious diseases and discuss its potential for future applications. Notably, CAR cell therapies, initially developed for cancer treatment, are gaining recognition as potential remedies for infectious diseases. The review sheds light on significant progress in CAR T cell therapy directed at viral and opportunistic fungal infections.
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Affiliation(s)
- Elena Morte-Romea
- Infectious Diseases Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
| | - Cecilia Pesini
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
- Immunotherapy, Cytotoxicity, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - Galadriel Pellejero-Sagastizábal
- Infectious Diseases Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
| | - Santiago Letona-Giménez
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
| | - Luis Martínez-Lostao
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Department of Immunology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Department of Microbiology, Pediatry, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
- Nanoscience Institute of Aragon (INA), Consejo Superior de Investigaciones Científicas (CSIC), University of Zaragoza, Zaragoza, Spain
| | - Silvia Loscos Aranda
- Infectious Diseases Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
| | - Carla Toyas
- Infectious Diseases Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
| | - Sergio Redrado
- Instituto de Carboquímica-Consejo Superior de Investigaciones Científicadas (ICB-CSIC), Zaragoza, Spain
| | - Elena Dolader-Ballesteros
- Department of Microbiology, Pediatry, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Maykel Arias
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
- Instituto de Carboquímica-Consejo Superior de Investigaciones Científicadas (ICB-CSIC), Zaragoza, Spain
| | - Eva M. Galvez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
- Instituto de Carboquímica-Consejo Superior de Investigaciones Científicadas (ICB-CSIC), Zaragoza, Spain
| | - Rebeca Sanz-Pamplona
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos III (CIBERESP), Madrid, Spain
| | - Julián Pardo
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
- Department of Microbiology, Pediatry, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Jose Ramón Paño-Pardo
- Infectious Diseases Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
| | - Ariel Ramírez-Labrada
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), Madrid, Spain
- Unidad de Nanotoxicología e Inmunotoxicología Experimental (UNATI), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
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Sun MY, Li W, Chen W. Chimeric antigen receptor T cell and regulatory T cell therapy in non-oncology diseases: A narrative review of studies from 2017 to 2023. Hum Vaccin Immunother 2023; 19:2251839. [PMID: 37814513 PMCID: PMC10566417 DOI: 10.1080/21645515.2023.2251839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/10/2023] [Indexed: 10/11/2023] Open
Abstract
Recently, the remarkable success of chimeric antigen receptor T cell (CAR-T) therapy in treating certain tumors has led to numerous studies exploring its potential application to treat non-oncology diseases. This review discusses the progress and evolution of CAR-T cell therapies for treating non-oncology diseases over the past 5 years. Additionally, we summarize the advantages and disadvantages of CAR-T cell therapy in treating non-oncological diseases and identify any difficulties that should be overcome. After conducting an in-depth analysis of the most recent studies on CAR-T technology, we discuss the key elements of CAR-T therapy, such as developing an effective CAR design for non-oncological diseases, controlling the rate and duration of response, and implementing safety measures to reduce toxicity. These studies provide new insights into different delivery strategies, the discovery of new target molecules, and improvements in the safety of CAR-T therapy for non-oncological diseases.
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Affiliation(s)
- Ming-Yao Sun
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences - Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
- Department of Clinical Nutrition, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
| | - Wanyang Li
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences - Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
| | - Wei Chen
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences - Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
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3
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Abdelaziz MO, Raftery MJ, Weihs J, Bielawski O, Edel R, Köppke J, Vladimirova D, Adler JM, Firsching T, Voß A, Gruber AD, Hummel LV, Fernandez Munoz I, Müller-Marquardt F, Willimsky G, Elleboudy NS, Trimpert J, Schönrich G. Early protective effect of a ("pan") coronavirus vaccine (PanCoVac) in Roborovski dwarf hamsters after single-low dose intranasal administration. Front Immunol 2023; 14:1166765. [PMID: 37520530 PMCID: PMC10372429 DOI: 10.3389/fimmu.2023.1166765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the danger posed by human coronaviruses. Rapid emergence of immunoevasive variants and waning antiviral immunity decrease the effect of the currently available vaccines, which aim at induction of neutralizing antibodies. In contrast, T cells are marginally affected by antigen evolution although they represent the major mediators of virus control and vaccine protection against virus-induced disease. Materials and methods We generated a multi-epitope vaccine (PanCoVac) that encodes the conserved T cell epitopes from all structural proteins of coronaviruses. PanCoVac contains elements that facilitate efficient processing and presentation of PanCoVac-encoded T cell epitopes and can be uploaded to any available vaccine platform. For proof of principle, we cloned PanCoVac into a non-integrating lentivirus vector (NILV-PanCoVac). We chose Roborovski dwarf hamsters for a first step in evaluating PanCoVac in vivo. Unlike mice, they are naturally susceptible to SARS-CoV-2 infection. Moreover, Roborovski dwarf hamsters develop COVID-19-like disease after infection with SARS-CoV-2 enabling us to look at pathology and clinical symptoms. Results Using HLA-A*0201-restricted reporter T cells and U251 cells expressing a tagged version of PanCoVac, we confirmed in vitro that PanCoVac is processed and presented by HLA-A*0201. As mucosal immunity in the respiratory tract is crucial for protection against respiratory viruses such as SARS-CoV-2, we tested the protective effect of single-low dose of NILV-PanCoVac administered via the intranasal (i.n.) route in the Roborovski dwarf hamster model of COVID-19. After infection with ancestral SARS-CoV-2, animals immunized with a single-low dose of NILV-PanCoVac i.n. did not show symptoms and had significantly decreased viral loads in the lung tissue. This protective effect was observed in the early phase (2 days post infection) after challenge and was not dependent on neutralizing antibodies. Conclusion PanCoVac, a multi-epitope vaccine covering conserved T cell epitopes from all structural proteins of coronaviruses, might protect from severe disease caused by SARS-CoV-2 variants and future pathogenic coronaviruses. The use of (HLA-) humanized animal models will allow for further efficacy studies of PanCoVac-based vaccines in vivo.
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Affiliation(s)
- Mohammed O. Abdelaziz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin J. Raftery
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julian Weihs
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatrics, Division of Gastroenterology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olivia Bielawski
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard Edel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Köppke
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Julia M. Adler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Theresa Firsching
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Luca V. Hummel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivan Fernandez Munoz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francesca Müller-Marquardt
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Partner Site Berlin, Berlin, Germany
| | - Nooran S. Elleboudy
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Günther Schönrich
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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4
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Jiang Y, Li SC. Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires. Brief Bioinform 2023; 24:7031156. [PMID: 36752378 DOI: 10.1093/bib/bbad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/09/2023] Open
Abstract
T-cell receptors (TCRs) play an essential role in the adaptive immune system. Probabilistic models for TCR repertoires can help decipher the underlying complex sequence patterns and provide novel insights into understanding the adaptive immune system. In this work, we develop TCRpeg, a deep autoregressive generative model to unravel the sequence patterns of TCR repertoires. TCRpeg largely outperforms state-of-the-art methods in estimating the probability distribution of a TCR repertoire, boosting the average accuracy from 0.672 to 0.906 measured by the Pearson correlation coefficient. Furthermore, with promising performance in probability inference, TCRpeg improves on a range of TCR-related tasks: profiling TCR repertoire probabilistically, classifying antigen-specific TCRs, validating previously discovered TCR motifs, generating novel TCRs and augmenting TCR data. Our results and analysis highlight the flexibility and capacity of TCRpeg to extract TCR sequence information, providing a novel approach for deciphering complex immunogenomic repertoires.
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Affiliation(s)
- Yuepeng Jiang
- Department of Computer science, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Shuai Cheng Li
- Department of Computer science, City University of Hong Kong, Kowloon Tong, Hong Kong
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Comparison of Two Commercially Available Interferon-γ Release Assays for T-Cell-Mediated Immunity and Evaluation of Humoral Immunity against SARS-CoV-2 in Healthcare Workers. Diagnostics (Basel) 2023; 13:diagnostics13040637. [PMID: 36832126 PMCID: PMC9955378 DOI: 10.3390/diagnostics13040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Cellular immunity against SARS-CoV-2 is an important component of the immune response to the virus. At present, two such tests based on interferon-gamma release (interferon-γ release assays, IGRAs) are available-Quan-T-Cell SARS-CoV-2 by EUROIMMUN and T-SPOT.COVID by Oxford Immunotec. In this paper, we compared the results of these two tests in 90 subjects employed at the Public Health Institute Ostrava who had previously undergone COVID-19 infection or were vaccinated against that disease. To the best of our knowledge, this is the first head-to-head comparison of these two tests evaluating T-cell-mediated immunity against SARS-CoV-2. In addition, we also evaluated humoral immunity in the same individuals using the in-house virus neutralization test and IgG ELISA assay. The evaluation yielded similar results for both IGRAs, with Quan-T-Cell appearing to be insignificantly (p = 0.08) more sensitive (all 90 individuals were at least borderline positive) than T-SPOT.COVID (negative results found in five patients). The overall qualitative (presence/absence of immune response) agreement of both tests with virus neutralization test and anti-S IgG was also excellent (close or equal to 100% in all subgroups, with the exception of unvaccinated Omicron convalescents, a large proportion of whom, i.e., four out of six subjects, were IgG negative while at least borderline positive for T-cell-mediated immunity measured by Quan-T). This implies that the evaluation of T-cell-mediated immunity is a more sensitive indicator of immune response than the evaluation of IgG seropositivity. This is true at least for unvaccinated patients with a history of being infected only by the Omicron variant, but also likely for other groups of patients.
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Mateyka LM, Strobl PM, Jarosch S, Scheu SJC, Busch DH, D'Ippolito E. Gene Signatures of T-Cell Activation Can Serve as Predictors of Functionality for SARS-CoV-2-Specific T-Cell Receptors. Vaccines (Basel) 2022; 10:vaccines10101617. [PMID: 36298482 PMCID: PMC9611811 DOI: 10.3390/vaccines10101617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
The importance of T cells in controlling SARS-CoV-2 infections has been demonstrated widely, but insights into the quality of these responses are still limited due to technical challenges. Indeed, understanding the functionality of the T-cell receptor (TCR) repertoire of a polyclonal antigen-specific population still requires the tedious work of T-cell cloning or TCR re-expression and subsequent characterization. In this work, we show that it is possible to discriminate highly functional and bystander TCRs based on gene signatures of T-cell activation induced by recent peptide stimulation. SARS-CoV-2-specific TCRs previously identified by cytokine release after peptide restimulation and subsequent single-cell RNA sequencing were re-expressed via CRISPR-Cas9-mediated gene editing into a Jurkat-based reporter cell line system suitable for high-throughput screening. We could observe differences in SARS-CoV-2 epitope recognition as well as a wide range of functional avidities. By correlating these in vitro TCR engineered functional data with the transcriptomic profiles of the corresponding TCR-expressing parental T cells, we could validate that gene signatures of recent T-cell activation accurately identify and predict truly SARS-CoV-2-specific TCRs. In summary, this work paves the way for alternative approaches useful for the functional analysis of global antigen-specific TCR repertoires with largely improved throughput.
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Affiliation(s)
- Laura M Mateyka
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Philipp M Strobl
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sebastian J C Scheu
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
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Pandey A, Madan R, Singh S. Immunology to Immunotherapeutics of SARS-CoV-2: Identification of Immunogenic Epitopes for Vaccine Development. Curr Microbiol 2022; 79:306. [PMID: 36064873 PMCID: PMC9444117 DOI: 10.1007/s00284-022-03003-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 08/16/2022] [Indexed: 11/21/2022]
Abstract
The emergence of COVID19 pandemic caused by SARS-CoV-2 virus has created a global public health and socio-economic crisis. Immunoinformatics-based approaches to investigate the potential antigens is the fastest way to move towards a multiepitope-based vaccine development. This review encompasses the underlying mechanisms of pathogenesis, innate and adaptive immune signaling along with evasion pathways of SARS-CoV-2. Furthermore, it compiles the promiscuous peptides from in silico studies which are subjected to prediction of cytokine milieu using web-based servers. Out of the 434 peptides retrieved from all studies, we have identified 33 most promising T cell vaccine candidates. This review presents a list of the most potential epitopes from several proteins of the virus based on their immunogenicity, homology, conservancy and population coverage studies. These epitopes can form a basis of second generation of vaccine development as the first generation vaccines in various stages of trials mostly focus only on Spike protein. We therefore, propose them as most potential candidates which can be taken up immediately for confirmation by experimental studies.
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Affiliation(s)
- Apoorva Pandey
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, P.O. Box No. 4911, New Delhi, 110029 India
| | - Riya Madan
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, Sahibzada Ajit Singh Nagar, Punjab 140306 India
| | - Swati Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
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Longitudinal Assessment of SARS-CoV-2-Specific T Cell Cytokine-Producing Responses for 1 Year Reveals Persistence of Multicytokine Proliferative Responses, with Greater Immunity Associated with Disease Severity. J Virol 2022; 96:e0050922. [PMID: 35699447 PMCID: PMC9278147 DOI: 10.1128/jvi.00509-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cell-mediated immunity is critical for long-term protection against most viral infections, including coronaviruses. We studied 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected survivors over a 1-year post-symptom onset (PSO) interval by ex vivo cytokine enzyme-linked immunosorbent spot assay (ELISpot) assay. All subjects demonstrated SARS-CoV-2-specific gamma interferon (IFN-γ), interleukin 2 (IL-2), and granzyme B (GzmB) T cell responses at presentation, with greater frequencies in severe disease. Cytokines, mainly produced by CD4+ T cells, targeted all structural proteins (nucleocapsid, membrane, and spike) except envelope, with GzmB and IL-2 greater than IFN-γ. Mathematical modeling predicted that (i) cytokine responses peaked at 6 days for IFN-γ, 36 days for IL-2, and 7 days for GzmB, (ii) severe illness was associated with reduced IFN-γ and GzmB but increased IL-2 production rates, and (iii) males displayed greater production of IFN-γ, whereas females produced more GzmB. Ex vivo responses declined over time, with persistence of IL-2 in 86% and of IFN-γ and GzmB in 70% of subjects at a median of 336 days PSO. The average half-life of SARS-CoV-2-specific cytokine-producing cells was modeled to be 139 days (~4.6 months). Potent T cell proliferative responses persisted throughout observation, were CD4 dominant, and were capable of producing all 3 cytokines. Several immunodominant CD4 and CD8 epitopes identified in this study were shared by seasonal coronaviruses or SARS-CoV-1 in the nucleocapsid and membrane regions. Both SARS-CoV-2-specific CD4+ and CD8+ T cell clones were able to kill target cells, though CD8 tended to be more potent. IMPORTANCE Our findings highlight the relative importance of SARS-CoV-2-specific GzmB-producing T cell responses in SARS-CoV-2 control and shared CD4 and CD8 immunodominant epitopes in seasonal coronaviruses or SARS-CoV-1, and they indicate robust persistence of T cell memory at least 1 year after infection. Our findings should inform future strategies to induce T cell vaccines against SARS-CoV-2 and other coronaviruses.
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9
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Krishna BA, Lim EY, Mactavous L, Lyons PA, Doffinger R, Bradley JR, Smith KGC, Sinclair J, Matheson NJ, Lehner PJ, Wills MR, Sithole N. Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID. EBioMedicine 2022; 81:104129. [PMID: 35772216 PMCID: PMC9235296 DOI: 10.1016/j.ebiom.2022.104129] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND There is currently no consensus on the diagnosis, definition, symptoms, or duration of COVID-19 illness. The diagnostic complexity of Long COVID is compounded in many patients who were or might have been infected with SARS-CoV-2 but not tested during the acute illness and/or are SARS-CoV-2 antibody negative. METHODS Given the diagnostic conundrum of Long COVID, we set out to investigate SARS-CoV-2-specific T cell responses in patients with confirmed SARS-CoV-2 infection and/or Long COVID from a cohort of mostly non-hospitalised patients. FINDINGS We discovered that IL-2 release (but not IFN-γ release) from T cells in response to SARS-CoV-2 peptides is both sensitive (75% +/-13%) and specific (88%+/-7%) for previous SARS-CoV-2 infection >6 months after a positive PCR test. We identified that 42-53% of patients with Long COVID, but without detectable SARS-CoV-2 antibodies, nonetheless have detectable SARS-CoV-2 specific T cell responses. INTERPRETATION Our study reveals evidence (detectable T cell mediated IL-2 release) of previous SARS-CoV-2 infection in seronegative patients with Long COVID. FUNDING This work was funded by the Addenbrooke's Charitable Trust (900276 to NS), NIHR award (G112259 to NS) and supported by the NIHR Cambridge Biomedical Research Centre. NJM is supported by the MRC (TSF MR/T032413/1) and NHSBT (WPA15-02). PJL is supported by the Wellcome Trust (PRF 210688/Z/18/Z, 084957/Z/08/Z), a Medical Research Council research grant MR/V011561/1 and the United Kingdom Research and a Innovation COVID Immunology Consortium grant (MR/V028448/1).
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Affiliation(s)
- Benjamin A Krishna
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Eleanor Y Lim
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Lenette Mactavous
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Cambridge NIHR BioResource Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; Department of Renal Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John Sinclair
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; NHS Blood and Transplant, Cambridge CB2 0PT, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Nyaradzai Sithole
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
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10
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Moga E, Lynton-Pons E, Domingo P. The Robustness of Cellular Immunity Determines the Fate of SARS-CoV-2 Infection. Front Immunol 2022; 13:904686. [PMID: 35833134 PMCID: PMC9271749 DOI: 10.3389/fimmu.2022.904686] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 12/11/2022] Open
Abstract
Two years after the appearance of the SARS-CoV-2 virus, the causal agent of the current global pandemic, it is time to analyze the evolution of the immune protection that infection and vaccination provide. Cellular immunity plays an important role in limiting disease severity and the resolution of infection. The early appearance, breadth and magnitude of SARS-CoV-2 specific T cell response has been correlated with disease severity and it has been thought that T cell responses may be sufficient to clear infection with minimal disease in COVID-19 patients with X-linked or autosomal recessive agammaglobulinemia. However, our knowledge of the phenotypic and functional diversity of CD8+ cytotoxic lymphocytes, CD4+ T helper cells, mucosal-associated invariant T (MAIT) cells and CD4+ T follicular helper (Tfh), which play a critical role in infection control as well as long-term protection, is still evolving. It has been described how CD8+ cytotoxic lymphocytes interrupt viral replication by secreting antiviral cytokines (IFN-γ and TNF-α) and directly killing infected cells, negatively correlating with stages of disease progression. In addition, CD4+ T helper cells have been reported to be key pieces, leading, coordinating and ultimately regulating antiviral immunity. For instance, in some more severe COVID-19 cases a dysregulated CD4+ T cell signature may contribute to the greater production of pro-inflammatory cytokines responsible for pathogenic inflammation. Here we discuss how cellular immunity is the axis around which the rest of the immune system components revolve, since it orchestrates and leads antiviral response by regulating the inflammatory cascade and, as a consequence, the innate immune system, as well as promoting a correct humoral response through CD4+ Tfh cells. This review also analyses the critical role of cellular immunity in modulating the development of high-affinity neutralizing antibodies and germinal center B cell differentiation in memory and long-lived antibody secreting cells. Finally, since there is currently a high percentage of vaccinated population and, in some cases, vaccine booster doses are even being administered in certain countries, we have also summarized newer approaches to long-lasting protective immunity and the cross-protection of cellular immune response against SARS-CoV-2.
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Affiliation(s)
- Esther Moga
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain,*Correspondence: Esther Moga,
| | - Elionor Lynton-Pons
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Domingo
- Unidad de enfermedades infecciosas, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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11
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Zavvar M, Yahyapoor A, Baghdadi H, Zargaran S, Assadiasl S, Abdolmohammadi K, Hossein Abooei A, Reza Sattarian M, JalaliFarahani M, Zarei N, Farahvash A, Fatahi Y, Deniz G, Zarebavani M, Nicknam MH. COVID-19 immunotherapy: Treatment based on the immune cell-mediated approaches. Int Immunopharmacol 2022; 107:108655. [PMID: 35248946 PMCID: PMC8872837 DOI: 10.1016/j.intimp.2022.108655] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Multiple efforts are currently underway to control and treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) worldwide. Despite all efforts, the virus that emerged in Wuhan city has rapidly spread globally and led to a public health emergency of international concern (PHEIC) due to the lack of approved antiviral therapy. Nevertheless, SARS-CoV-2 has had a significant influence on the evolution of cellular therapeutic approaches. Adoptive immune cell therapy is innovative and offers either promising prophylactic or therapy for patients with moderate-to-severe COVID-19. This approach is aimed at developing safety and providing secure and effective therapy in combination with standard therapy for all COVID-19 infected individuals. Based on the effective results of previous studies on both inflammatory and autoimmune diseases, various immune cell therapies against COVID-19 have been reviewed and discussed. It must be considered that the application of cell therapy for treatment and to eliminate infected respiratory cells could result in excessive inflammation, so this treatment must be used in combination with other treatments, despite its many beneficial efforts.
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12
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Nattrass RG, Krafft L, Zjablovskaja P, Schuster M, Kasmapour B, Sarisoy C, Minich J, Bach E, Streeck H. The effect of age on the magnitude and longevity of Th1-directed CD4 T cell responses to SARS-CoV-2. Immunology 2022; 166:327-340. [PMID: 35396852 PMCID: PMC9111694 DOI: 10.1111/imm.13475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 11/26/2022] Open
Abstract
Age is associated with changes in the immune system which increase the risk for severe COVID‐19. Here, we investigate SARS‐CoV‐2‐reactive CD4 T cells from individuals recovered from SARS‐CoV‐2 infection with mild COVID‐19 symptoms after 3, 6 and 9 months using incubation with SARS‐CoV‐2 S1, S2 and N‐peptide pools, followed by flow cytometry for a Th1‐activation profile or proliferation analyses. We found that SARS‐CoV‐2‐reactive CD4 T cells are decreasing on average after 9 months but highly polyfunctional CD4 T cells can peak after 6‐month recovery. We show that individuals older than 60 years of age have significantly more SARS‐CoV‐2‐reactive T cells in their blood after 3 months of recovery compared to younger individuals and that the percentage of SARS‐CoV‐2‐reactive Th1‐directed CD4 T cells in the blood of mild‐COVID‐19‐recovered individuals correlates with age. Finally, we show that individuals over the age of 40 have significantly increased the amounts of highly polyfunctional SARS‐CoV‐2‐S‐peptide‐reactive CD4 T cells, compared to SARS‐CoV‐2 naïve individuals, than those under the age of 40. These findings suggest that in individuals recovered from mild COVID‐19, increased age is associated with significantly more highly polyfunctional SARS‐CoV‐2‐reactive CD4 T cells with a Th1‐profile and that these responses persist over time.
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Affiliation(s)
- Ryan G. Nattrass
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
| | - Lisa Krafft
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
| | | | | | | | - Cem Sarisoy
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
| | - Jessica Minich
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
| | - Elena Bach
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
| | - Hendrik Streeck
- Institute of VirologyUniversity Hospital BonnBonnGermany
- German Centre for Infection Research (DZIF)partner site Bonn‐CologneBraunschweigGermany
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13
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Kumar S, Saxena SK, Maurya VK, Tripathi AK. Progress and Challenges Toward Generation and Maintenance of Long-Lived Memory T Lymphocyte Responses During COVID-19. Front Immunol 2022; 12:804808. [PMID: 35250966 PMCID: PMC8891701 DOI: 10.3389/fimmu.2021.804808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease 2019 (COVID-19) pandemic is a serious global threat until we identify the effective preventive and therapeutic strategies. SARS-CoV-2 infection is characterized by various immunopathological consequences including lymphocyte activation and dysfunction, lymphopenia, cytokine storm, increased level of neutrophils, and depletion and exhaustion of lymphocytes. Considering the low level of antibody-mediated protection during coronavirus infection, understanding the role of T cell for long-term protection is decisive. Both CD4+ and CD8+ T cell response is imperative for cell-mediated immune response during COVID-19. However, the level of CD8+ T cell response reduced to almost half as compared to CD4+ after 6 months of infection. The long-term protection is mediated via generation of immunological memory response during COVID-19. The presence of memory CD4+ T cells in all the severely infected and recovered individuals shows that the memory response is predominated by CD4+ T cells. Prominently, the antigen-specific CD4+ and CD8+ T cells are specifically observed during day 0 to day 28 in COVID-19-vaccinated individuals. However, level of antigen-specific T memory cells in COVID-19-vaccinated individuals defines the long-term protection against forthcoming outbreaks of SARS-CoV-2.
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Affiliation(s)
- Swatantra Kumar
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Shailendra K Saxena
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Vimal K Maurya
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
| | - Anil K Tripathi
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India
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14
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T cell responses to SARS-CoV-2 in humans and animals. J Microbiol 2022; 60:276-289. [PMID: 35157219 PMCID: PMC8852923 DOI: 10.1007/s12275-022-1624-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2, the causative agent of COVID-19, first emerged in 2019. Antibody responses against SARS-CoV-2 have been given a lot of attention. However, the armamentarium of humoral and T cells may have differing roles in different viral infections. Though the exact role of T cells in COVID-19 remains to be elucidated, prior experience with human coronavirus has revealed an essential role of T cells in the outcomes of viral infections. Moreover, an increasing body of evidence suggests that T cells might be effective against SARS-CoV-2. This review summarizes the role of T cells in mouse CoV, human pathogenic respiratory CoV in general and SARS-CoV-2 in specific.
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15
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Park H, Park MS, Seok JH, You J, Kim J, Kim J, Park MS. Insights into the immune responses of SARS-CoV-2 in relation to COVID-19 vaccines. J Microbiol 2022; 60:308-320. [PMID: 35235179 PMCID: PMC8890016 DOI: 10.1007/s12275-022-1598-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/24/2021] [Accepted: 12/31/2021] [Indexed: 12/14/2022]
Abstract
The three types of approved coronavirus disease 2019 (COVID-19) vaccines that have been emergency-use listed (EUL) by the World Health Organization are mRNA vaccines, adenovirus-vectored vaccines, and inactivated vaccines. Canonical vaccine developments usually take years or decades to be completed to commercialization; however, the EUL vaccines being used in the current situation comprise several COVID-19 vaccine candidates applied in studies and clinical settings across the world. The extraordinary circumstances of the COVID-19 pandemic have necessitated the emergency authorization of these EUL vaccines, which have been rapidly developed. Although the benefits of the EUL vaccines outweigh their adverse effects, there have been reports of rare but fatal cases directly associated with COVID-19 vaccinations. Thus, a reassessment of the immunological rationale underlying EUL vaccines in relation to COVID-19 caused by SARSCOV-2 virus infection is now required. In this review, we discuss the manifestations of COVID-19, immunologically projected effects of EUL vaccines, reported immune responses, informed issues related to COVID-19 vaccination, and the potential strategies for future vaccine use against antigenic variants.
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Affiliation(s)
- Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Mee Sook Park
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jong Hyeon Seok
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jaehwan You
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jineui Kim
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jeonghun Kim
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Chung Mong-Koo Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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16
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Kudlay D, Kofiadi I, Khaitov M. Peculiarities of the T Cell Immune Response in COVID-19. Vaccines (Basel) 2022; 10:242. [PMID: 35214700 PMCID: PMC8877307 DOI: 10.3390/vaccines10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the T cell response to SARS-CoV-2 is critical to vaccine development, epidemiological surveillance, and control strategies for this disease. This review provides data from studies of the immune response in coronavirus infections. It describes general mechanisms of immunity, its T cell components, and presents a detailed scheme of the T cell response in SARS-CoV-2 infection, including from the standpoint of determining the most promising targets for assessing its level. In addition, we reviewed studies investigating post-vaccination immunity in the development of vaccines against COVID-19. This review also includes the peculiarities of immunity in different age and gender groups, and in the presence of a number of factors, for example, comorbidity or disease severity. This study summarizes the most informative methods for assessing the immune response to SARS-CoV-2 infection.
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Affiliation(s)
- Dmitry Kudlay
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Ilya Kofiadi
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Immunology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Musa Khaitov
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Immunology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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17
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Identification of cytotoxic T cells and their T cell receptor sequences targeting COVID-19 using MHC class I-binding peptides. J Hum Genet 2022; 67:411-419. [PMID: 35110673 PMCID: PMC8807680 DOI: 10.1038/s10038-022-01013-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022]
Abstract
Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) was first reported in China in December 2019, various variants have been identified in different areas of the world such as United Kingdom (alpha), South Africa (beta and omicron), Brazil (gamma), and India (delta). Some of SARS-CoV-2 variants, each of which is characterized by a unique mutation(s) in spike protein, are concerned due to their high infectivity and the capability to escape from neutralizing antibodies elicited by vaccinations. To identify peptide epitopes that are derived from SARS-CoV-2 viral proteins and possibly induce CD8+ T cell immunity, we investigated SARS-CoV-2-derived peptides that are likely to bind to major histocompatibility complex (MHC) class I molecules. We identified a total of 15 peptides that bind to human leukocyte antigen (HLA)-A*24:02, HLA-A*02:01, or HLA-A*02:06, and possibly induce cytotoxic T lymphocytes (CTLs); thirteen of them corresponded to ORF1ab polyprotein, one peptide to spike protein and the remaining one to membrane glycoprotein. CD8+ T cells that recognize these peptides were detected in peripheral blood samples in three individuals recovered from COVID-19 as well as non-infected individuals. Since most of these peptides are commonly conserved among other coronaviruses including SARS-CoV and/or MERS-CoV, these might be useful to maintain T cell responses to coronaviruses that are pandemic at present and will become the future threat. We could define pairs of TRA and TRB sequences of nine CTL clones that recognize SARS-CoV-2-derived peptides. We might use these SARS-CoV-2-derived peptide-reactive TCR sequences for investigating the history of SARS-CoV-2 infection.
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18
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Li Y, Hu J, Wang Y, Liu D, Shi Y, Zhang J, Liu Y, Lin D, Lin J, Hu W, He H, Wang W, Fan W, Li L, Wang D, Wang K, Xu J. T-Cell Repertoire Characteristics of Asymptomatic and Re-Detectable Positive COVID-19 Patients. Front Immunol 2022; 12:769442. [PMID: 35154070 PMCID: PMC8828559 DOI: 10.3389/fimmu.2021.769442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/24/2021] [Indexed: 01/01/2023] Open
Abstract
The prevention of the COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear. Here we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different courses, including asymptomatic, symptomatic, convalescent, and re-detectable positive cases. We identified a set of V-J gene combinations characterizing the upward immune responses through asymptomatic and symptomatic courses. Furthermore, some of these V-J combinations could be awakened in the re-detectable positive cases, which may help predict the risk of recurrent infection. Therefore, TCR repertoire examination has the potential to strengthen the clinical surveillance and the immunotherapy development for COVID-19.
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Affiliation(s)
- Yizhe Li
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jian Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongsi Wang
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dongdong Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaling Shi
- Department of Laboratory Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaqi Zhang
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongzi Lin
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Jing Lin
- Department of Clinical Laboratory, The First People’s Hospital of Foshan, Foshan, China
| | - Wei Hu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Haolan He
- Department of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Wentao Fan
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Linlin Li
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dawei Wang
- Department of Pulmonary and Critical Care Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Kejian Wang
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianhua Xu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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19
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Francis JM, Leistritz-Edwards D, Dunn A, Tarr C, Lehman J, Dempsey C, Hamel A, Rayon V, Liu G, Wang Y, Wille M, Durkin M, Hadley K, Sheena A, Roscoe B, Ng M, Rockwell G, Manto M, Gienger E, Nickerson J, Moarefi A, Noble M, Malia T, Bardwell PD, Gordon W, Swain J, Skoberne M, Sauer K, Harris T, Goldrath AW, Shalek AK, Coyle AJ, Benoist C, Pregibon DC. Allelic variation in class I HLA determines CD8 + T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2. Sci Immunol 2022; 7:eabk3070. [PMID: 34793243 PMCID: PMC9017864 DOI: 10.1126/sciimmunol.abk3070] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Effective presentation of antigens by HLA class I molecules to CD8+ T cells is required for viral elimination and generation of long-term immunological memory. In this study, we applied a single-cell, multi-omic technology to generate a unified ex vivo characterization of the CD8+ T cell response to SARS-CoV-2 across 4 major HLA class I alleles. We found that HLA genotype conditions key features of epitope specificity, TCR α/β sequence diversity, and the utilization of pre-existing SARS-CoV-2 reactive memory T cell pools. Single-cell transcriptomics revealed functionally diverse T cell phenotypes of SARS-CoV-2-reactive T cells, associated with both disease stage and epitope specificity. Our results show that HLA variations significantly influence the CD8+ T cell repertoire shape and utilization of immune recall upon SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gang Liu
- Repertoire Immune Medicines, Cambridge, MA, USA
| | | | | | | | - Kane Hadley
- Repertoire Immune Medicines, Cambridge, MA, USA
| | | | | | - Mark Ng
- Repertoire Immune Medicines, Cambridge, MA, USA
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- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Tim Harris
- Repertoire Immune Medicines, Cambridge, MA, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, San Diego, CA, USA
| | - Alex K Shalek
- Repertoire Immune Medicines, Cambridge, MA, USA.,Department of Chemistry and Koch Institute for Integrative Cancer Research, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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20
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Larionova R, Byvaltsev K, Kravtsova О, Takha E, Petrov S, Kazarian G, Valeeva A, Shuralev E, Mukminov M, Renaudineau Y, Arleevskaya M. SARS-Cov2 acute and post-active infection in the context of autoimmune and chronic inflammatory diseases. J Transl Autoimmun 2022; 5:100154. [PMID: 35434592 PMCID: PMC9005220 DOI: 10.1016/j.jtauto.2022.100154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022] Open
Abstract
The clinical and immunological spectrum of acute and post-active COVID-19 syndrome overlaps with criteria used to characterize autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). Indeed, following SARS-Cov2 infection, the innate immune response is altered with an initial delayed production of interferon type I (IFN-I), while the NF-kappa B and inflammasome pathways are activated. In lung and digestive tissues, an alternative and extrafollicular immune response against SARS-Cov2 takes place with, consequently, an altered humoral and memory T cell response leading to breakdown of tolerance with the emergence of autoantibodies. However, the risk of developing severe COVID-19 among SLE and RA patients did not exceed the general population except in those having pre-existing neutralizing autoantibodies against IFN-I. Treatment discontinuation rather than COVID-19 infection or vaccination increases the risk of developing flares. Last but not least, a limited number of case reports of individuals having developed SLE or RA following COVID-19 infection/vaccination have been reported. Altogether, the SARS-Cov2 pandemic represents an unique opportunity to investigate the dangerous interplay between the immune response against infectious agents and autoimmunity, and to better understand the triggering role of infection as a risk factor in autoimmune and chronic inflammatory disease development.
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Key Words
- ACE2, angiotensin converting enzyme 2
- ACPA, anti-cyclic citrullinated peptide autoAb
- ANA, antinuclear autoAb
- AutoAb, autoantibodies
- BAFF/BlySS, B-cell-activating factor/B lymphocyte stimulator
- CCL, chemokine ligand
- COVID-19, coronavirus disease 2019
- DMARDs, disease-modifying anti-rheumatic drugs
- E, envelope
- HEp-2, human epithelioma cell line 2
- IFN-I, interferon type I
- IFNAR, IFN-alpha receptors
- IL, interleukin
- IRF, interferon regulatory factor
- ISGs, IFN-stimulated genes
- ITP, immune-thrombocytopenic purpura
- Ig, immunoglobulin
- Infection
- Inflammation
- Jak, Janus kinase
- LDH, lactate dehydrogenase
- M, membrane
- MDA-5, melanoma differentiation-associated protein
- MERS-Cov, Middle East respiratory syndrome coronavirus
- MIS-C, multisystem inflammatory syndrome in children
- N, nucleocapsid
- NET, nuclear extracellular traps
- NF-κB, nuclear factor-kappa B
- NK, natural killer
- NLRP3, NOD-like receptor family
- Rheumatoid arthritis
- Risk factors
- SARS-Cov2
- Systemic lupus erythematosus
- T cell receptor, TLR
- Toll-like receptor, TMPRSS2
- aPL, antiphospholipid
- mAb, monoclonal Ab
- open reading frame, PACS
- pathogen-associated molecular patterns, pDC
- pattern recognition receptors, RA
- peptidylarginine deiminase 4, PAMPs
- plasmacytoid dendritic cells, PMN
- polymorphonuclear leukocytes, PRRs
- post-active COVID-19 syndrome, PAD-4
- primary Sjögren's syndrome, SLE
- pyrin domain containing 3, ORF
- reactive oxygen species, rt-PCR
- receptor binding domain, RF
- regulatory T cells, VDJ
- retinoic acid-inducible gene I, ROS
- reverse transcription polymerase chain reaction, S
- rheumatoid arthritis, RBD
- rheumatoid factor, RIG-I
- severe acute respiratory coronavirus 2, SjS
- signal transducer and activator of transcription, TCR
- single-stranded ribonucleic acid, STAT
- spike, SAD
- systemic autoimmune disease, SARS-Cov2
- systemic lupus erythematosus, SSc
- systemic sclerosis, ssRNA
- transmembrane serine protease 2, TNF
- tumor necrosis factor, Treg
- variable, diversity and joining Ig genes
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Affiliation(s)
- Regina Larionova
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - K Byvaltsev
- Institute of Fundamental Medicine, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Оlga Kravtsova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Elena Takha
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
| | - Sergei Petrov
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Gevorg Kazarian
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
| | - Anna Valeeva
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
| | - Eduard Shuralev
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, Kazan, Russia
- Kazan State Academy of Veterinary Medicine Named After N.E. Bauman, Kazan, Russia
| | - Malik Mukminov
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Yves Renaudineau
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Laboratory of Immunology, CHU Purpan Toulouse, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France
| | - Marina Arleevskaya
- Central Research Laboratory, Kazan State Medical Academy, Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
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21
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Wagner KI, Mateyka LM, Jarosch S, Grass V, Weber S, Schober K, Hammel M, Burrell T, Kalali B, Poppert H, Beyer H, Schambeck S, Holdenrieder S, Strötges-Achatz A, Haselmann V, Neumaier M, Erber J, Priller A, Yazici S, Roggendorf H, Odendahl M, Tonn T, Dick A, Witter K, Mijočević H, Protzer U, Knolle PA, Pichlmair A, Crowell CS, Gerhard M, D'Ippolito E, Busch DH. Recruitment of highly cytotoxic CD8 + T cell receptors in mild SARS-CoV-2 infection. Cell Rep 2021; 38:110214. [PMID: 34968416 PMCID: PMC8677487 DOI: 10.1016/j.celrep.2021.110214] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/07/2021] [Accepted: 12/13/2021] [Indexed: 01/12/2023] Open
Abstract
T cell immunity is crucial for control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and has been studied widely on a quantitative level. However, the quality of responses, in particular of CD8+ T cells, has only been investigated marginally so far. Here, we isolate T cell receptor (TCR) repertoires specific for immunodominant SARS-CoV-2 epitopes restricted to common human Leukocyte antigen (HLA) class I molecules in convalescent individuals. SARS-CoV-2-specific CD8+ T cells are detected up to 12 months after infection. TCR repertoires are diverse, with heterogeneous functional avidity and cytotoxicity toward virus-infected cells, as demonstrated for TCR-engineered T cells. High TCR functionality correlates with gene signatures that, remarkably, could be retrieved for each epitope:HLA combination analyzed. Overall, our data demonstrate that polyclonal and highly functional CD8+ TCRs—classic features of protective immunity—are recruited upon mild SARS-CoV-2 infection, providing tools to assess the quality of and potentially restore functional CD8+ T cell immunity.
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Affiliation(s)
- Karolin I Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Laura M Mateyka
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Simone Weber
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Teresa Burrell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Behnam Kalali
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Holger Poppert
- Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany; Neurologische Klinik, University Hospital Rechts der Isar, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Henriette Beyer
- Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany
| | - Sophia Schambeck
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technical University of Munich (TUM), 80636 Munich, Germany
| | - Andrea Strötges-Achatz
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technical University of Munich (TUM), 80636 Munich, Germany
| | - Verena Haselmann
- Department of Clinical Chemistry, University Medicine Mannheim, Medical Faculty Mannheim of the University of Heidelberg, 68167 Mannheim, Germany
| | - Michael Neumaier
- Department of Clinical Chemistry, University Medicine Mannheim, Medical Faculty Mannheim of the University of Heidelberg, 68167 Mannheim, Germany
| | - Johanna Erber
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Alina Priller
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sarah Yazici
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Hedwig Roggendorf
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Marcus Odendahl
- Experimental Transfusion Medicine, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, 01307 Dresden, Germany
| | - Torsten Tonn
- Experimental Transfusion Medicine, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, 01307 Dresden, Germany
| | - Andrea Dick
- Laboratory of Immunogenetics and Molecular Diagnostics, Department of Transfusion Medicine, Cellular Therapeutics and Hemostaseology, LMU University Hospital, 81377 Munich, Germany
| | - Klaus Witter
- Laboratory of Immunogenetics and Molecular Diagnostics, Department of Transfusion Medicine, Cellular Therapeutics and Hemostaseology, LMU University Hospital, 81377 Munich, Germany
| | - Hrvoje Mijočević
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Claudia S Crowell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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22
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Monzavi SM, Naderi M, Ahmadbeigi N, Kajbafzadeh AM, Muhammadnejad S. An outlook on antigen-specific adoptive immunotherapy for viral infections with a focus on COVID-19. Cell Immunol 2021; 367:104398. [PMID: 34217004 PMCID: PMC8214814 DOI: 10.1016/j.cellimm.2021.104398] [Citation(s) in RCA: 2] [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: 01/29/2021] [Revised: 05/23/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022]
Abstract
Although not a standard-of-care yet, adoptive immunotherapeutic approaches have gradually earned a place within the list of antiviral therapies for some of fatal and hard-to-treat viral diseases. To maintain robust antiviral immunity and to effectively target the viral particles and virally-infected cells, immune cells capable of recognizing the viral antigens are required. While conventional vaccination can induce these cells in vivo; another option is to prime and generate antigen-specific immune cells ex vivo. This approach has been successfully trialed for virulent opportunistic viral infections after bone marrow transplantation. Amid the crisis of SARS-CoV2 pandemic, which has been followed by the success of certain early-authorized vaccines; some institutions and companies have explored the effects of viral-specific adoptive cell transfers (ACTs) in trials, as alternative treatments. Aimed at outlining a perspective on antigen-specific adoptive immunotherapy for viral infections, this review article specifically provides an appraisal of ACT-based studies/trials on SARS-CoV2 infection.
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Affiliation(s)
- Seyed Mostafa Monzavi
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran; Pediatric Urology and Regenerative Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Naderi
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Ahmadbeigi
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdol-Mohammad Kajbafzadeh
- Pediatric Urology and Regenerative Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Samad Muhammadnejad
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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23
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Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O'Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med 2021; 13:101. [PMID: 34127050 PMCID: PMC8201469 DOI: 10.1186/s13073-021-00910-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). METHODS We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. RESULTS From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. CONCLUSIONS Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kelly S Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kaylee M Gentry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Allison Woods
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Brandon Carpenter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Sandor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
- Institute for Inflammatory Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Division of Medical Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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24
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Esmaeilzadeh A, Elahi R. Immunobiology and immunotherapy of COVID-19: A clinically updated overview. J Cell Physiol 2021; 236:2519-2543. [PMID: 33022076 PMCID: PMC7675260 DOI: 10.1002/jcp.30076] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new member of the coronavirus family that can cause coronavirus disease 2019 (COVID-19). COVID-9 has become a global pandemic with severe health issues around the world. Identifying the accurate immunopathogenesis of the COVID-19 and the immune response against SARS-CoV-2 is necessary for the development of therapeutic approaches and rational drug design. This paper aims to overview the updated clinical data on the immunopathogenesis of the COVID-19 and review the innate and adaptive immune response to SARS-CoV-2. Also, challenges of the immune response to SARS-CoV-2 leading to dysfunctional immune response and their contribution to the progression of the disease have been discussed. To achieve a more efficient immune response, multiple methods could be applied, including regulation of the immune response, augmentation of the immune system against the virus, inhibition of the dysfunctional immune checkpoints, and inhibition of the viral replication/infection. Based on the immune response against SARS-CoV-2 and its dysfunction, we introduce potential immunotherapies as well as reviewing recruiting/completed clinical trials of COVID-19.
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Affiliation(s)
- Abdolreza Esmaeilzadeh
- Department of Immunology, School of MedicineZanjan University of Medical SciencesZanjanIran
- Immunotherapy Research and Technology GroupZanjan University of Medical SciencesZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical SciencesZanjanIran
| | - Reza Elahi
- Zanjan University of Medical SciencesZanjanIran
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25
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Ferrantelli F, Chiozzini C, Manfredi F, Giovannelli A, Leone P, Federico M. Simultaneous CD8 + T-Cell Immune Response against SARS-Cov-2 S, M, and N Induced by Endogenously Engineered Extracellular Vesicles in Both Spleen and Lungs. Vaccines (Basel) 2021; 9:240. [PMID: 33801926 PMCID: PMC7999804 DOI: 10.3390/vaccines9030240] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/29/2022] Open
Abstract
Most advanced vaccines against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 are designed to induce antibodies against spike (S) protein. Differently, we developed an original strategy to induce CD8+ T cytotoxic lymphocyte (CTL) immunity based on in vivo engineering of extracellular vesicles (EVs). This is a new vaccination approach based on intramuscular injection of DNA expression vectors coding for a biologically inactive HIV-1 Nef protein (Nefmut) with an unusually high efficiency of incorporation into EVs, even when foreign polypeptides are fused to its C-terminus. Nanovesicles containing Nefmut-fused antigens released by muscle cells can freely circulate into the body and are internalized by antigen-presenting cells. Therefore, EV-associated antigens can be cross-presented to prime antigen-specific CD8+ T-cells. To apply this technology to a strategy of anti-SARS-CoV-2 vaccine, we designed DNA vectors expressing the products of fusion between Nefmut and different viral antigens, namely N- and C-terminal moieties of S (referred to as S1 and S2), M, and N. We provided evidence that all fusion products are efficiently uploaded in EVs. When the respective DNA vectors were injected in mice, a strong antigen-specific CD8+ T cell immunity became detectable in spleens and, most important, in lung airways. Co-injection of DNA vectors expressing the diverse SARS-CoV-2 antigens resulted in additive immune responses in both spleen and lungs. Hence, DNA vectors expressing Nefmut-based fusion proteins can be proposed for new anti-SARS-CoV-2 vaccine strategies.
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Affiliation(s)
- Flavia Ferrantelli
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Chiara Chiozzini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Francesco Manfredi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Andrea Giovannelli
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Patrizia Leone
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Maurizio Federico
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
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26
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Abdullahi IN, Emeribe AU, Adekola HA, Abubakar SD, Dangana A, Shuwa HA, Nwoba ST, Mustapha JO, Haruna MT, Olowookere KA, Animasaun OS, Ugwu CE, Onoja SO, Gadama AS, Mohammed M, Daneji IM, Amadu DO, Ghamba PE, Onukegbe NB, Shehu MS, Isomah C, Babayo A, Ahmad AEF. Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges. Hum Vaccin Immunother 2021; 17:620-637. [PMID: 32936732 PMCID: PMC7993231 DOI: 10.1080/21645515.2020.1812313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measures, the pandemic continues to spread. It has been widely accepted that preventive vaccination strategies are the public health measures for countering this pandemic. This study critically reviews the latest scientific advancement in genomics, replication pattern, pathogenesis, and immunopathology of SARS-CoV-2 infection and how these concepts could be used in the development of vaccines. We also offer a detailed discussion on the anticipated potency, efficacy, safety, and pharmaco-economic issues that are and will be associated with candidate COVID-19 vaccines.
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Affiliation(s)
- Idris Nasir Abdullahi
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Anthony Uchenna Emeribe
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | | | - Sharafudeen Dahiru Abubakar
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Amos Dangana
- Department of Medical Laboratory Services, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Halima Ali Shuwa
- Lydia Becker Institute of Immunology, Manchester Collaborative Center for Inflammation Research, Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | | | - Jelili Olaide Mustapha
- Biological Sciences Department, Faculty of Science, University of Alberta, Edmonton, Canada
| | | | - Kafayat Adepeju Olowookere
- Department of Medical Laboratory Services, Ladoke Akintola University of Technology Teaching Hospital, Ogbomoso, Nigeria
| | - Olawale Sunday Animasaun
- Nigeria Field Epidemiology and Laboratory Training Programme, African Field Epidemiology Network, Abuja, Nigeria
| | - Charles Egede Ugwu
- Department of Medical Laboratory Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Abdullahi Sani Gadama
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Musa Mohammed
- Department of Medicine, Immunology Unit, Ahmadu Bello University, Zaria, Nigeria
| | - Isa Muhammad Daneji
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Dele Ohinoyi Amadu
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Peter Elisha Ghamba
- WHO National Polio Reference Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | | | - Muhammad Sagir Shehu
- Medical Laboratory Department, College of Health Technology, Ningi, Bauchi State, Nigeria
| | - Chiladi Isomah
- Medical Laboratory Science Department, Rivers State University, Port Harcourt, Nigeria
| | - Adamu Babayo
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Abdurrahman El-Fulaty Ahmad
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
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27
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Steinbuck MP, Seenappa LM, Jakubowski A, McNeil LK, Haqq CM, DeMuth PC. A lymph node-targeted Amphiphile vaccine induces potent cellular and humoral immunity to SARS-CoV-2. SCIENCE ADVANCES 2021; 7:7/6/eabe5819. [PMID: 33547083 PMCID: PMC7864572 DOI: 10.1126/sciadv.abe5819] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/17/2020] [Indexed: 05/17/2023]
Abstract
The profound consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mandate urgent development of effective vaccines. Here, we evaluated an Amphiphile (AMP) vaccine adjuvant, AMP-CpG, composed of diacyl lipid-modified CpG, admixed with the SARS-CoV-2 Spike-2 receptor binding domain protein as a candidate vaccine (ELI-005) in mice. AMP modification efficiently delivers CpG to lymph nodes, where innate and adaptive immune responses are generated. Compared to alum, immunization with AMP-CpG induced >25-fold higher antigen-specific T cells that produced multiple T helper 1 (TH1) cytokines and trafficked into lung parenchyma. Antibody responses favored TH1 isotypes (IgG2c and IgG3) and potently neutralized Spike-2-ACE2 receptor binding, with titers 265-fold higher than natural convalescent patient COVID-19 responses; T cell and antibody responses were maintained despite 10-fold dose reduction in Spike antigen. Both cellular and humoral immune responses were preserved in aged mice. These advantages merit clinical translation to SARS-CoV-2 and other protein subunit vaccines.
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MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/immunology
- Female
- HEK293 Cells
- Humans
- Immunity, Cellular
- Immunity, Humoral
- Immunogenicity, Vaccine
- Lymph Nodes/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Neutralization Tests
- Oligodeoxyribonucleotides/administration & dosage
- Oligodeoxyribonucleotides/immunology
- Protein Interaction Domains and Motifs/immunology
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Surface-Active Agents/administration & dosage
- Treatment Outcome
- Vaccination/methods
- Vaccines, Subunit/immunology
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Affiliation(s)
- Martin P Steinbuck
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA
| | - Lochana M Seenappa
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA
| | - Aniela Jakubowski
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA
| | - Lisa K McNeil
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA
| | - Christopher M Haqq
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA.
| | - Peter C DeMuth
- Elicio Therapeutics, One Kendall Square, Suite 14303, Cambridge, MA 02139, USA
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28
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Ward D, Higgins M, Phelan JE, Hibberd ML, Campino S, Clark TG. An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Genome Med 2021; 13:4. [PMID: 33413610 PMCID: PMC7790334 DOI: 10.1186/s13073-020-00822-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online "immuno-analytics" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).
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Affiliation(s)
- Daniel Ward
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Matthew Higgins
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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29
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Minervina AA, Komech EA, Titov A, Bensouda Koraichi M, Rosati E, Mamedov IZ, Franke A, Efimov GA, Chudakov DM, Mora T, Walczak AM, Lebedev YB, Pogorelyy MV. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection. eLife 2021; 10:e63502. [PMID: 33399535 PMCID: PMC7806265 DOI: 10.7554/elife.63502] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However, neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T-cell response nor the diversity of resulting immune memory is well understood. In this study, we use longitudinal high-throughput T-cell receptor (TCR) sequencing to track changes in the T-cell repertoire following two mild cases of COVID-19. In both donors, we identified CD4+ and CD8+ T-cell clones with transient clonal expansion after infection. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurrence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors, the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T-cell clones were detected in the memory fraction at the pre-infection time point, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.
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Affiliation(s)
| | - Ekaterina A Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Aleksei Titov
- National Research Center for HematologyMoscowRussian Federation
| | - Meriem Bensouda Koraichi
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel UniversityKielGermany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Masaryk University, Central European Institute of TechnologyBrnoCzech Republic
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and PerinatologyMoscowRussian Federation
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel UniversityKielGermany
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Masaryk University, Central European Institute of TechnologyBrnoCzech Republic
| | - Thierry Mora
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Moscow State UniversityMoscowRussian Federation
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
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30
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Chen Y, Klein SL, Garibaldi BT, Li H, Wu C, Osevala NM, Li T, Margolick JB, Pawelec G, Leng SX. Aging in COVID-19: Vulnerability, immunity and intervention. Ageing Res Rev 2021; 65:101205. [PMID: 33137510 PMCID: PMC7604159 DOI: 10.1016/j.arr.2020.101205] [Citation(s) in RCA: 527] [Impact Index Per Article: 175.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic was first reported in Wuhan, China in December 2019, moved across the globe at an unprecedented speed, and is having a profound and yet still unfolding health and socioeconomic impacts. SARS-CoV-2, a β-coronavirus, is a highly contagious respiratory pathogen that causes a disease that has been termed the 2019 coronavirus disease (COVID-19). Clinical experience thus far indicates that COVID-19 is highly heterogeneous, ranging from being asymptomatic and mild to severe and causing death. Host factors including age, sex, and comorbid conditions are key determinants of disease severity and progression. Aging itself is a prominent risk factor for severe disease and death from COVID-19. We hypothesize that age-related decline and dysregulation of immune function, i.e., immunosenescence and inflammaging play a major role in contributing to heightened vulnerability to severe COVID-19 outcomes in older adults. Much remains to be learned about the immune responses to SARS-CoV-2 infection. We need to begin partitioning all immunological outcome data by age to better understand disease heterogeneity and aging. Such knowledge is critical not only for understanding of COVID-19 pathogenesis but also for COVID-19 vaccine development.
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Affiliation(s)
- Yiyin Chen
- Guangdong Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States
| | - Brian T Garibaldi
- Division of Pulmonary and Critical Care Medicine and Johns Hopkins Biocontainment Unit, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Huifen Li
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cunjin Wu
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Geriatrics, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Nicole M Osevala
- Division of Geriatrics, Department of Medicine, Pennsylvania State University School of Medicine, Hershey, PA, United States
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Joseph B Margolick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States
| | - Graham Pawelec
- Department of Immunology, University of Tübingen, Tübingen, Germany; Health Sciences North Research Institute, Sudbury, ON, Canada
| | - Sean X Leng
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States; Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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31
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Kim DS, Rowland-Jones S, Gea-Mallorquí E. Will SARS-CoV-2 Infection Elicit Long-Lasting Protective or Sterilising Immunity? Implications for Vaccine Strategies (2020). Front Immunol 2020; 11:571481. [PMID: 33362759 PMCID: PMC7756008 DOI: 10.3389/fimmu.2020.571481] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
In December 2019, an outbreak of a novel coronavirus (SARS-CoV-2) in Wuhan, China resulted in the current COVID-19 global pandemic. The human immune system has not previously encountered this virus, raising the important question as to whether or not protective immunity is generated by infection. Growing evidence suggests that protective immunity can indeed be acquired post-infection-although a handful of reinfection cases have been reported. However, it is still unknown whether the immune response to SARS-CoV-2 leads to some degree of long-lasting protection against the disease or the infection. This review draws insights from previous knowledge regarding the nature and longevity of immunity to the related virus, SARS-CoV, to fill the gaps in our understanding of the immune response to SARS-CoV-2. Deciphering the immunological characteristics that give rise to protective immunity against SARS-CoV-2 is critical to guiding vaccine development and also predicting the course of the pandemic. Here we discuss the recent evidence that characterises the adaptive immune response against SARS-CoV-2 and its potential implications for the generation of memory responses and long-term protection.
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Affiliation(s)
- David S. Kim
- Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sarah Rowland-Jones
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ester Gea-Mallorquí
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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32
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Taefehshokr N, Taefehshokr S, Heit B. Mechanisms of Dysregulated Humoral and Cellular Immunity by SARS-CoV-2. Pathogens 2020; 9:E1027. [PMID: 33302366 PMCID: PMC7762606 DOI: 10.3390/pathogens9121027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic, a disease caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), was first identified in December 2019 in China, and has led to thousands of mortalities globally each day. While the innate immune response serves as the first line of defense, viral clearance requires activation of adaptive immunity, which employs B and T cells to provide sanitizing immunity. SARS-CoV-2 has a potent arsenal of mechanisms used to counter this adaptive immune response through processes, such as T cells depletion and T cell exhaustion. These phenomena are most often observed in severe SARS-CoV-2 patients, pointing towards a link between T cell function and disease severity. Moreover, neutralizing antibody titers and memory B cell responses may be short lived in many SARS-CoV-2 patients, potentially exposing these patients to re-infection. In this review, we discuss our current understanding of B and T cells immune responses and activity in SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, ON N0M 2N0, Canada;
| | - Sina Taefehshokr
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51368, Iran;
| | - Bryan Heit
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, ON N0M 2N0, Canada;
- Robarts Research Institute, London, ON N6A 5K8, Canada
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33
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Payen D, Cravat M, Maadadi H, Didelot C, Prosic L, Dupuis C, Losser MR, De Carvalho Bittencourt M. A Longitudinal Study of Immune Cells in Severe COVID-19 Patients. Front Immunol 2020; 11:580250. [PMID: 33178207 PMCID: PMC7597438 DOI: 10.3389/fimmu.2020.580250] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/02/2020] [Indexed: 01/09/2023] Open
Abstract
Little is known about the time-dependent immune responses in severe COVID-19. Data of 15 consecutive patients were sequentially recorded from intensive care unit admission. Lymphocyte subsets and total monocyte and subsets counts were monitored as well as the expression of HLA-DR. For 5 patients, SARS-CoV-2-specific T-cell polyfunctionality was assessed against Spike and Nucleoprotein SARS-CoV-2 peptides. Non-specific inflammation markers were increased in all patients. Median monocyte HLA-DR expression was below the 8,000 AB/C threshold defining acquired immunodepression. A "V" trend curve for lymphopenia, monocyte numbers, and HLA-DR expression was observed with a nadir between days 11 and 14 after symptoms' onset. Intermediate CD14++CD16+ monocytes increased early with a reduction in classic CD14++CD16- monocytes. Polyfunctional SARS-Cov-2-specific CD4 T-cells were present and functional, whereas virus-specific CD8 T-cells were less frequent and not efficient. We report a temporal variation of both innate and adaptive immunity in severe COVID-19 patients, helpful in guiding therapeutic decisions (e.g. anti-inflammatory vs. immunostimulatory ones). We describe a defect in virus-specific CD8 T-cells, a potential biomarker of clinical severity. These combined data also provide helpful knowledge for vaccine design. CLINICAL TRIAL REGISTRATION https://clinicaltrials.gov/, identifier NCT04386395.
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Affiliation(s)
- Didier Payen
- Université Paris 7 Denis Diderot, UMR 1160 INSERM, Paris, France
| | - Maxime Cravat
- Université de Lorraine, CHRU-Nancy, Laboratoire d’Immunologie, Nancy, France
| | - Hadil Maadadi
- Université de Lorraine, CHRU-Nancy, Département d’Anesthésie Réanimation Brabois Adulte, Nancy, France
| | - Carole Didelot
- CHRU-Nancy, Plateforme de Cytométrie en Flux Diagnostique, Nancy, France
| | - Lydia Prosic
- CHRU-Nancy, Plateforme de Cytométrie en Flux Diagnostique, Nancy, France
| | - Claire Dupuis
- Service de Médecine Intensive et Réanimation, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Marie-Reine Losser
- Université de Lorraine, CHRU-Nancy, Département d’Anesthésie Réanimation Brabois Adulte, Nancy, France
- Université de Lorraine, INSERM UMR 1116, Nancy, France
| | - Marcelo De Carvalho Bittencourt
- Université de Lorraine, CHRU-Nancy, Laboratoire d’Immunologie, Nancy, France
- CHRU-Nancy, Plateforme de Cytométrie en Flux Diagnostique, Nancy, France
- Université de Lorraine, CNRS UMR 7365, IMoPA, Nancy, France
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34
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Mishra S. Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201141. [PMID: 33047062 PMCID: PMC7540743 DOI: 10.1098/rsos.201141] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/01/2020] [Indexed: 05/05/2023]
Abstract
Novel coronavirus, SARS-CoV-2, has emerged as one of the deadliest pathogens of this century, creating an unprecedented pandemic. Belonging to the betacoronavirus family, it primarily spreads through human contact via symptomatic and asymptomatic transmission. Despite several attempts since it emerged, there is no known treatment in the form of drugs or vaccines. Hence, work on developing a potential multi-subunit vaccine is the need of the hour. In this study, attempts have been made to find globally conserved epitopes from the entire set of SARS-CoV-2 proteins as there is as yet, no clear information on the immunogenicity of these proteins. Using diverse computational tools, a ranked list of probable immunogenic, promiscuous epitopes generated through all the three main stages of antigen processing and presentation pathways has been prioritized. Moreover, several useful insights were gleaned during these analyses. One of the most important insights is that all of the proteins in this pathogen present unique epitopes, so that the targeting of a few specific viral proteins is not likely to result in an effective immune response in humans. Due to the presence of these unique epitopes in all of the SARS-CoV-2 proteins, stronger immune responses generated by T cell hyperactivation may lead to cytokine storm and immunopathology and consequently, remote chances of human survival. These epitopes, after due validation in vitro, may thus need to be presented to the human body in that form of multi-subunit epitope-based vaccine that avoids such immunopathologies.
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Affiliation(s)
- Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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35
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Melenotte C, Silvin A, Goubet AG, Lahmar I, Dubuisson A, Zumla A, Raoult D, Merad M, Gachot B, Hénon C, Solary E, Fontenay M, André F, Maeurer M, Ippolito G, Piacentini M, Wang FS, Ginhoux F, Marabelle A, Kroemer G, Derosa L, Zitvogel L. Immune responses during COVID-19 infection. Oncoimmunology 2020; 9:1807836. [PMID: 32939324 PMCID: PMC7480812 DOI: 10.1080/2162402x.2020.1807836] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 02/09/2023] Open
Abstract
Over the past 16 years, three coronaviruses (CoVs), severe acute respiratory syndrome CoV (SARS-CoV) in 2002, Middle East respiratory syndrome CoV (MERS-CoV) in 2012 and 2015, and SARS-CoV-2 in 2020, have been causing severe and fatal human epidemics. The unpredictability of coronavirus disease-19 (COVID-19) poses a major burden on health care and economic systems across the world. This is caused by the paucity of in-depth knowledge of the risk factors for severe COVID-19, insufficient diagnostic tools for the detection of SARS-CoV-2, as well as the absence of specific and effective drug treatments. While protective humoral and cellular immune responses are usually mounted against these betacoronaviruses, immune responses to SARS-CoV2 sometimes derail towards inflammatory tissue damage, leading to rapid admissions to intensive care units. The lack of knowledge on mechanisms that tilt the balance between these two opposite outcomes poses major threats to many ongoing clinical trials dealing with immunostimulatory or immunoregulatory therapeutics. This review will discuss innate and cognate immune responses underlying protective or deleterious immune reactions against these pathogenic coronaviruses.
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Affiliation(s)
- Cléa Melenotte
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Infectious Diseases, IHU-Méditerranée Infection, Marseille, France
| | | | - Anne-Gaëlle Goubet
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Imran Lahmar
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Agathe Dubuisson
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, University College London, National Institute for Health Research Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Didier Raoult
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Mansouria Merad
- Service de Urgences et de Permanence des Soins, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
| | | | | | - Eric Solary
- Immunology, Gustave Roussy, Villejuif, France
| | - Michaela Fontenay
- INSERM U1016, Centre National Recherche Scientifique (CNRS) UMR8104, Institut Cochin, Université de Paris, Paris, France
| | | | - Markus Maeurer
- Immunosurgery, Immunotherapy Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
- Med Clinic, University of Mainz, Mayence, Germany
| | - Giuseppe Ippolito
- Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases “Lazzaro Spallanzani” I.R.C.C.S., Rome, Italy
| | - Mauro Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- Infectious Diseases Department, National Institute for Infectious Disease IRCCS “Lazzaro Spallanzani”, Rome, Italy
| | - Fu-Sheng Wang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Aurélien Marabelle
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie,Pathologie – PUI – Hygiène, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Lisa Derosa
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Laurence Zitvogel
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
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Kothari A, Singh V, Nath UK, Kumar S, Rai V, Kaushal K, Omar BJ, Pandey A, Jain N. Immune Dysfunction and Multiple Treatment Modalities for the SARS-CoV-2 Pandemic: Races of Uncontrolled Running Sweat? BIOLOGY 2020; 9:E243. [PMID: 32846906 PMCID: PMC7563789 DOI: 10.3390/biology9090243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic threat with more than 11.8 million confirmed cases and more than 0.5 million deaths as of 3 July 2020. Given the lack of definitive pharmaceutical interventions against SARS-CoV-2, multiple therapeutic strategies and personal protective applications are being used to reduce the risk of high mortality and community spread of this infection. Currently, more than a hundred vaccines and/or alternative therapeutic regimens are in clinical trials, and some of them have shown promising results in improving the immune cell environment and controlling the infection. In this review, we discussed high-performance multi-directory strategies describing the uncontrolled deregulation of the host immune landscape associated with coronavirus disease (COVID-19) and treatment strategies using an anti-neoplastic regimen. We also followed selected current treatment plans and the most important on-going clinical trials and their respective outcomes for blocking SARS-CoV-2 pathogenesis through regenerative medicine, such as stem cell therapy, chimeric antigen receptors, natural killer (NK) cells, extracellular vesicular-based therapy, and others including immunomodulatory regimens, anti-neoplastic therapy, and current clinical vaccine therapy.
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Affiliation(s)
- Ashish Kothari
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India; (A.K.); (V.S.)
| | - Vanya Singh
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India; (A.K.); (V.S.)
| | - Uttam Kumar Nath
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Sandeep Kumar
- School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Vineeta Rai
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA;
| | - Karanvir Kaushal
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India; (A.K.); (V.S.)
| | - Atul Pandey
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Neeraj Jain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh 249203, India;
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37
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Lebeau G, Vagner D, Frumence É, Ah-Pine F, Guillot X, Nobécourt E, Raffray L, Gasque P. Deciphering SARS-CoV-2 Virologic and Immunologic Features. Int J Mol Sci 2020; 21:E5932. [PMID: 32824753 PMCID: PMC7460647 DOI: 10.3390/ijms21165932] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 and its associated pathology, COVID-19, have been of particular concerns these last months due to the worldwide burden they represent. The number of cases requiring intensive care being the critical point in this epidemic, a better understanding of the pathophysiology leading to these severe cases is urgently needed. Tissue lesions can be caused by the pathogen or can be driven by an overwhelmed immune response. Focusing on SARS-CoV-2, we and others have observed that this virus can trigger indeed an immune response that can be dysregulated in severe patients and leading to further injury to multiple organs. The purpose of the review is to bring to light the current knowledge about SARS-CoV-2 virologic and immunologic features. Thus, we address virus biology, life cycle, tropism for many organs and how ultimately it will affect several host biological and physiological functions, notably the immune response. Given that therapeutic avenues are now highly warranted, we also discuss the immunotherapies available to manage the infection and the clinical outcomes.
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Affiliation(s)
- Grégorie Lebeau
- Unité de Recherche Études Pharmaco-Immunologiques, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France; (D.V.); (É.F.); (X.G.); (P.G.)
- Laboratoire de Biologie, Secteur Laboratoire d’immunologie Clinique et Expérimentale de la Zone de l’océan Indien (LICE-OI), Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France
| | - Damien Vagner
- Unité de Recherche Études Pharmaco-Immunologiques, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France; (D.V.); (É.F.); (X.G.); (P.G.)
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249, Platform CYROI, 2 rue Maxime Rivière, 97491 Sainte Clotilde, La Réunion, France
| | - Étienne Frumence
- Unité de Recherche Études Pharmaco-Immunologiques, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France; (D.V.); (É.F.); (X.G.); (P.G.)
- Laboratoire de Biologie, Secteur Laboratoire d’immunologie Clinique et Expérimentale de la Zone de l’océan Indien (LICE-OI), Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France
| | - Franck Ah-Pine
- Service d’anatomo-Pathologie, Centre Hospitalier Universitaire Sud Réunion, 97410 Saint Pierre, France;
| | - Xavier Guillot
- Unité de Recherche Études Pharmaco-Immunologiques, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France; (D.V.); (É.F.); (X.G.); (P.G.)
- Service de Rhumatologie, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France
| | - Estelle Nobécourt
- Service d’endocrinologie Diabétologie, Centre Hospitalier Universitaire Sud Réunion, 97410 Saint Pierre, France;
- Université de Formation et de Recherche Santé, Université de la Réunion, 97400 Saint-Denis, France
| | - Loïc Raffray
- Service de Médecine Interne, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France;
| | - Philippe Gasque
- Unité de Recherche Études Pharmaco-Immunologiques, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France; (D.V.); (É.F.); (X.G.); (P.G.)
- Laboratoire de Biologie, Secteur Laboratoire d’immunologie Clinique et Expérimentale de la Zone de l’océan Indien (LICE-OI), Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France
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38
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Sariol A, Perlman S. Lessons for COVID-19 Immunity from Other Coronavirus Infections. Immunity 2020; 53:248-263. [PMID: 32717182 PMCID: PMC7359787 DOI: 10.1016/j.immuni.2020.07.005] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022]
Abstract
A key goal to controlling coronavirus disease 2019 (COVID-19) is developing an effective vaccine. Development of a vaccine requires knowledge of what constitutes a protective immune response and also features that might be pathogenic. Protective and pathogenic aspects of the response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not well understood, partly because the virus has infected humans for only 6 months. However, insight into coronavirus immunity can be informed by previous studies of immune responses to non-human coronaviruses, common cold coronaviruses, and SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we review the literature describing these responses and discuss their relevance to the SARS-CoV-2 immune response.
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Affiliation(s)
- Alan Sariol
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Stanley Perlman
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA; Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA.
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Abstract
A key goal to controlling coronavirus disease 2019 (COVID-19) is developing an effective vaccine. Development of a vaccine requires knowledge of what constitutes a protective immune response and also features that might be pathogenic. Protective and pathogenic aspects of the response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not well understood, partly because the virus has infected humans for only 6 months. However, insight into coronavirus immunity can be informed by previous studies of immune responses to non-human coronaviruses, common cold coronaviruses, and SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we review the literature describing these responses and discuss their relevance to the SARS-CoV-2 immune response.
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Affiliation(s)
- Alan Sariol
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Stanley Perlman
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA; Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA.
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40
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Gutierrez L, Beckford J, Alachkar H. Deciphering the TCR Repertoire to Solve the COVID-19 Mystery. Trends Pharmacol Sci 2020; 41:518-530. [PMID: 32576386 PMCID: PMC7305739 DOI: 10.1016/j.tips.2020.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected several millions and killed more than quarter of a million worldwide to date. Important questions have remained unanswered: why some patients develop severe disease, while others do not; and what roles do genetic variabilities play in the individual immune response to this viral infection. Here, we discuss the critical role T cells play in the orchestration of the antiviral response underlying the pathogenesis of the disease, COVID-19. We highlight the scientific rationale for comprehensive and longitudinal TCR analyses in COVID-19 and reason that analyzing TCR repertoire in COVID-19 patients would reveal important findings that may explain the outcome disparity observed in these patients. Finally, we provide a framework describing the different strategies, the advantages, and the challenges involved in obtaining useful TCR repertoire data to advance our fight against COVID-19.
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Affiliation(s)
- Lucas Gutierrez
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - John Beckford
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089-9121, USA.
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41
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Kataria A, Yakubu I, Winstead R, Gowda M, Gupta G. COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice. Transplant Direct 2020; 6:e582. [PMID: 33134506 PMCID: PMC7581117 DOI: 10.1097/txd.0000000000001031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/13/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 was identified in the late 2019 as the cause of coronavirus disease 2019 (COVID-19), an acute respiratory viral illness. Patients with chronic underlying conditions may have an increased risk of morbidity and mortality from COVID-19. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. Early data suggest that the mortality of patients on dialysis may be comparable to those with kidney transplants, although more research is needed. This concise review aims to describe the epidemiology of COVID-19 in kidney transplant recipients, manifestations, appropriate management, and clinical outcomes based on the available literature. Current evidence on many of the specific antiviral measures against COVID-19 has not shown a clear-cut benefit in smaller studies and the results of several ongoing larger clinical trials are awaited. In addition, we also highlight the impact of COVID-19 on kidney transplant center practice and volumes; potential living or deceased donors, recipients; and induction immunosuppression and surgical strategies.
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Affiliation(s)
| | - Idris Yakubu
- Virginia Commonwealth University Health System, Richmond, VA
| | - Ryan Winstead
- Virginia Commonwealth University Health System, Richmond, VA
| | | | - Gaurav Gupta
- Virginia Commonwealth University Health System, Richmond, VA
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42
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Wang YT, Landeras-Bueno S, Hsieh LE, Terada Y, Kim K, Ley K, Shresta S, Saphire EO, Regla-Nava JA. Spiking Pandemic Potential: Structural and Immunological Aspects of SARS-CoV-2. Trends Microbiol 2020; 28:605-618. [PMID: 32507543 PMCID: PMC7237910 DOI: 10.1016/j.tim.2020.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023]
Abstract
SARS-Coronavirus-2 (SARS-CoV-2) causes Coronavirus disease 2019 (COVID-19), an infectious respiratory disease causing thousands of deaths and overwhelming public health systems. The international spread of SARS-CoV-2 is associated with the ease of global travel, and societal dynamics, immunologic naiveté of the host population, and muted innate immune responses. Based on these factors and the expanding geographic scale of the disease, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic-the first caused by a coronavirus. In this review, we summarize the current epidemiological status of COVID-19 and consider the virological and immunological lessons, animal models, and tools developed in response to prior SARS-CoV and MERS-CoV outbreaks that can serve as resources for development of SARS-CoV-2 therapeutics and vaccines. In particular, we discuss structural insights into the SARS-CoV-2 spike protein, a major determinant of transmissibility, and discuss key molecular aspects that will aid in understanding and fighting this new global threat.
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Affiliation(s)
| | | | - Li-En Hsieh
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yutaka Terada
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kenneth Kim
- Kord Animal Health Diagnostic Laboratory, Tennessee Department of Agriculture, Nashville, TN, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sujan Shresta
- La Jolla Institute for Immunology, La Jolla, CA, USA
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43
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SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 2020; 584:457-462. [PMID: 32668444 DOI: 10.1038/s41586-020-2550-z] [Citation(s) in RCA: 1364] [Impact Index Per Article: 341.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022]
Abstract
Memory T cells induced by previous pathogens can shape susceptibility to, and the clinical severity of, subsequent infections1. Little is known about the presence in humans of pre-existing memory T cells that have the potential to recognize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we studied T cell responses against the structural (nucleocapsid (N) protein) and non-structural (NSP7 and NSP13 of ORF1) regions of SARS-CoV-2 in individuals convalescing from coronavirus disease 2019 (COVID-19) (n = 36). In all of these individuals, we found CD4 and CD8 T cells that recognized multiple regions of the N protein. Next, we showed that patients (n = 23) who recovered from SARS (the disease associated with SARS-CoV infection) possess long-lasting memory T cells that are reactive to the N protein of SARS-CoV 17 years after the outbreak of SARS in 2003; these T cells displayed robust cross-reactivity to the N protein of SARS-CoV-2. We also detected SARS-CoV-2-specific T cells in individuals with no history of SARS, COVID-19 or contact with individuals who had SARS and/or COVID-19 (n = 37). SARS-CoV-2-specific T cells in uninfected donors exhibited a different pattern of immunodominance, and frequently targeted NSP7 and NSP13 as well as the N protein. Epitope characterization of NSP7-specific T cells showed the recognition of protein fragments that are conserved among animal betacoronaviruses but have low homology to 'common cold' human-associated coronaviruses. Thus, infection with betacoronaviruses induces multi-specific and long-lasting T cell immunity against the structural N protein. Understanding how pre-existing N- and ORF1-specific T cells that are present in the general population affect the susceptibility to and pathogenesis of SARS-CoV-2 infection is important for the management of the current COVID-19 pandemic.
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Singh VK, Mishra A, Singh S, Kumar P, Singh M, Jagannath C, Khan A. Emerging Prevention and Treatment Strategies to Control COVID-19. Pathogens 2020; 9:E501. [PMID: 32585805 PMCID: PMC7350294 DOI: 10.3390/pathogens9060501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has now become a serious global threat after inflicting more than 8 million infections and 425,000 deaths in less than 6 months. Currently, no definitive treatment or prevention therapy exists for COVID-19. The unprecedented rise of this pandemic has rapidly fueled research efforts to discover and develop new vaccines and treatment strategies against this novel coronavirus. While hundreds of vaccines/therapeutics are still in the preclinical or early stage of clinical development, a few of them have shown promising results in controlling the infection. Here, in this review, we discuss the promising vaccines and treatment options for COVID-19, their challenges, and potential alternative strategies.
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Affiliation(s)
- Vipul K. Singh
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (A.M.); (C.J.)
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (A.M.); (C.J.)
| | - Shubhra Singh
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.S.); (M.S.)
| | - Premranjan Kumar
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Manisha Singh
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.S.); (M.S.)
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (A.M.); (C.J.)
| | - Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (A.M.); (C.J.)
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45
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Sfera A, Osorio C, Jafri N, Diaz EL, Campo Maldonado JE. Intoxication With Endogenous Angiotensin II: A COVID-19 Hypothesis. Front Immunol 2020; 11:1472. [PMID: 32655579 PMCID: PMC7325923 DOI: 10.3389/fimmu.2020.01472] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 has spread rapidly around the globe. However, despite its high pathogenicity and transmissibility, the severity of the associated disease, COVID-19, varies widely. While the prognosis is favorable in most patients, critical illness, manifested by respiratory distress, thromboembolism, shock, and multi-organ failure, has been reported in about 5% of cases. Several studies have associated poor COVID-19 outcomes with the exhaustion of natural killer cells and cytotoxic T cells, lymphopenia, and elevated serum levels of D-dimer. In this article, we propose a common pathophysiological denominator for these negative prognostic markers, endogenous, angiotensin II toxicity. We hypothesize that, like in avian influenza, the outlook of COVID-19 is negatively correlated with the intracellular accumulation of angiotensin II promoted by the viral blockade of its degrading enzyme receptors. In this model, upregulated angiotensin II causes premature vascular senescence, leading to dysfunctional coagulation, and immunity. We further hypothesize that angiotensin II blockers and immune checkpoint inhibitors may be salutary for COVID-19 patients with critical illness by reversing both the clotting and immune defects (Graphical Abstract).
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Affiliation(s)
- Adonis Sfera
- Patton State Hospital, San Bernardino, CA, United States
| | - Carolina Osorio
- Department of Psychiatry, Loma Linda University, Loma Linda, CA, United States
| | - Nyla Jafri
- Patton State Hospital, San Bernardino, CA, United States
| | - Eddie Lee Diaz
- Patton State Hospital, San Bernardino, CA, United States
| | - Jose E Campo Maldonado
- Department of Medicine, The University of Texas Rio Grande Valley, Edinburg, TX, United States
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46
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Smith CC, Entwistle S, Willis C, Vensko S, Beck W, Garness J, Sambade M, Routh E, Olsen K, Kodysh J, O’Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and Selection of Vaccine Epitopes in SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.04.135004. [PMID: 32577654 PMCID: PMC7302209 DOI: 10.1101/2020.06.04.135004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner. In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2. We begin with an exploration of the space of possible T cell epitopes in SARS-CoV-2 with interrogation of predicted HLA-I and HLA-II ligands, overlap between predicted ligands, protein source, as well as concurrent human/murine coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles and co-localization of CD4+ and CD8+ T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. From 58 initial candidates, three B cell epitope regions were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials.
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Affiliation(s)
- Christof C. Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kelly Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Timothy O’Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, California
| | - Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G. Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, North Carolina
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, North Carolina
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
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Manners C, Larios Bautista E, Sidoti H, Lopez OJ. Protective Adaptive Immunity Against Severe Acute Respiratory Syndrome Coronaviruses 2 (SARS-CoV-2) and Implications for Vaccines. Cureus 2020; 12:e8399. [PMID: 32499988 PMCID: PMC7268578 DOI: 10.7759/cureus.8399] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging human coronavirus responsible for coronavirus disease 2019 (COVID-19), a predominantly respiratory disease that has become a global pandemic. Millions of people worldwide are suffering from COVID-19, and hundreds of thousands of those infected have died. Nevertheless, many more people who have been infected with SARS-CoV-2 are asymptomatic or suffer a mild disease characterized by dry cough and mild fever. This new pandemic poses a threat to public health on a global scale, and an intervention to prevent continued spread of SARS-CoV-2 virus is of the utmost importance. To assess preventive and therapeutic strategies, it is imperative to understand the pathogenesis and immune response against SARS-CoV-2. In this review, we concentrate on the protective adaptive immune response elicited by this novel coronavirus as well as requirements for a successful vaccine inducing optimal protection.
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Affiliation(s)
- Christopher Manners
- Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, USA
| | - Erick Larios Bautista
- Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, USA
| | - Hannah Sidoti
- Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, USA
| | - Osvaldo J Lopez
- Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, USA
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48
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A single-cell approach to engineer CD8+ T cells targeting cytomegalovirus. Cell Mol Immunol 2020; 18:1326-1328. [PMID: 32451452 PMCID: PMC7246339 DOI: 10.1038/s41423-020-0466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
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Rokni M, Ghasemi V, Tavakoli Z. Immune responses and pathogenesis of SARS-CoV-2 during an outbreak in Iran: Comparison with SARS and MERS. Rev Med Virol 2020; 30:e2107. [PMID: 32267987 PMCID: PMC7235481 DOI: 10.1002/rmv.2107] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
The beginning of 2020 has seen the emergence of COVID-19, an outbreak caused by a novel coronavirus, SARS-CoV-2, an important pathogen for humans. There is an urgent need to better understand this new virus and to develop ways to control its spread. In Iran, the first case of the COVID-19 was reported after spread from China and other countries. Fever, cough, and fatigue were the most common symptoms of this virus. In worldwide, the incubation period of COVID-19 was 3 to 7 days and approximately 80% of infections are mild or asymptomatic, 15% are severe, requiring oxygen, and 5% are critical infections, requiring ventilation. To mount an antiviral response, the innate immune system recognizes molecular structures that are produced by the invasion of the virus. COVID-19 infection induces IgG antibodies against N protein that can be detected by serum as early as day 4 after the onset of disease and with most patients seroconverting by day 14. Laboratory evidence of clinical patients showed that a specific T-cell response against SARS-CoV-2 is important for the recognition and killing of infected cells, particularly in the lungs of infected individuals. At present, there is no specific antiviral therapy for COVID-19 and the main treatments are supportive. In this review, we investigated the innate and acquired immune responses in patients who recovered from COVID-19, which could inform the design of prophylactic vaccines and immunotherapy for the future.
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Affiliation(s)
- Mohsen Rokni
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
- Department of Immunology, Buali Hospital of LaboratoryZahedan University of Medical SciencesZahedanIran
| | - Vida Ghasemi
- Student Research Committee, Department of Midwifery and Reproductive Health, School of Nursing and MidwiferyShahid Beheshti University of Medical SciencesTehranIran
- School of MedicineAsad Abad university of Medical SciencesHamadanIran
| | - Zahra Tavakoli
- Department of Virology, School of MedicineLorestan University of Medical SciencesKhoramabadIran
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50
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Ji W, Niu L, Peng W, Zhang Y, Cheng H, Gao F, Shi Y, Qi J, Gao GF, Liu WJ. Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner. Mol Immunol 2019; 112:274-282. [PMID: 31226552 PMCID: PMC7112684 DOI: 10.1016/j.molimm.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 11/28/2022]
Abstract
Crystal structure of HLA-B*4001 was determined. The salt bridges in HLA-B*4001 and H-2Kd have different structural characteristics. MHC I mutations that disrupt the salt bridge alleviate peptide binding. Mutations of the salt bridge-forming residues may impact TCR recognition, directly or indirectly.
The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2Kd in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I α helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells.
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Affiliation(s)
- Wei Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Ling Niu
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiyu Peng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yongli Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hao Cheng
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Shi
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - George F Gao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| | - William J Liu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
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