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Zheng K, Chong AY, Mentzer AJ. How could our genetics impact COVID-19 vaccine response? Expert Rev Clin Immunol 2024; 20:1027-1039. [PMID: 38676712 DOI: 10.1080/1744666x.2024.2346584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
INTRODUCTION The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has posed unprecedented global health challenges since its emergence in December 2019. The rapid availability of vaccines has been estimated to save millions of lives, but there is variation in how individuals respond to vaccines, influencing their effectiveness at an individual, and population level. AREAS COVERED This review focuses on human genetic factors influencing the immune response and effectiveness of vaccines, highlighting the importance of associations across the HLA locus. Genome-Wide Association Studies (GWAS) and other genetic association analyses have identified statistically significant associations between specific HLA alleles including HLA-DRB1*13, DBQ1*06, and A*03 impacting antibody responses and the risk of breakthrough infections post-vaccination. Relationships between these associations and potential mechanisms and links with risks of natural infection or disease are explored, and this review concludes by emphasizing how understanding the mechanisms of these genetic determinants may inform the development of tailored vaccination strategies. EXPERT OPINION Although complex, we believe these findings from the SARS-CoV2 pandemic offer a unique opportunity to understand the relationships between HLA and infection and vaccine response, with a goal of optimizing individual protection against COVID-19 in the ongoing pandemic, and possibly influencing wider vaccine development in the future.
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Affiliation(s)
- Keyi Zheng
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
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2
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Verstegen NJM, Hagen RR, Kreher C, Kuijper LH, Dijssel JVD, Ashhurst T, Kummer LYL, Palomares Cabeza V, Steenhuis M, Duurland MC, Jongh RD, Schoot CEVD, Konijn VAL, Mul E, Kedzierska K, van Dam KPJ, Stalman EW, Boekel L, Wolbink G, Tas SW, Killestein J, Rispens T, Wieske L, Kuijpers TW, Eftimov F, van Kempen ZLE, van Ham SM, Ten Brinke A, van de Sandt CE. T cell activation markers CD38 and HLA-DR indicative of non-seroconversion in anti-CD20-treated patients with multiple sclerosis following SARS-CoV-2 mRNA vaccination. J Neurol Neurosurg Psychiatry 2024; 95:855-864. [PMID: 38548324 DOI: 10.1136/jnnp-2023-332224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/19/2024] [Indexed: 08/18/2024]
Abstract
BACKGROUND Messenger RNA (mRNA) vaccines provide robust protection against SARS-CoV-2 in healthy individuals. However, immunity after vaccination of patients with multiple sclerosis (MS) treated with ocrelizumab (OCR), a B cell-depleting anti-CD20 monoclonal antibody, is not yet fully understood. METHODS In this study, deep immune profiling techniques were employed to investigate the immune response induced by SARS-CoV-2 mRNA vaccines in untreated patients with MS (n=21), OCR-treated patients with MS (n=57) and healthy individuals (n=30). RESULTS Among OCR-treated patients with MS, 63% did not produce detectable levels of antibodies (non-seroconverted), and those who did have lower spike receptor-binding domain-specific IgG responses compared with healthy individuals and untreated patients with MS. Before vaccination, no discernible immunological differences were observed between non-seroconverted and seroconverted OCR-treated patients with MS. However, non-seroconverted patients received overall more OCR infusions, had shorter intervals since their last OCR infusion and displayed higher OCR serum concentrations at the time of their initial vaccination. Following two vaccinations, non-seroconverted patients displayed smaller B cell compartments but instead exhibited more robust activation of general CD4+ and CD8+ T cell compartments, as indicated by upregulation of CD38 and HLA-DR surface expression, when compared with seroconverted patients. CONCLUSION These findings highlight the importance of optimising treatment regimens when scheduling SARS-CoV-2 vaccination for OCR-treated patients with MS to maximise their humoral and cellular immune responses. This study provides valuable insights for optimising vaccination strategies in OCR-treated patients with MS, including the identification of CD38 and HLA-DR as potential markers to explore vaccine efficacy in non-seroconverting OCR-treated patients with MS.
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Affiliation(s)
- Niels J M Verstegen
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth R Hagen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Christine Kreher
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisan H Kuijper
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jet van den Dijssel
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute, and The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Laura Y L Kummer
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Virginia Palomares Cabeza
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariël C Duurland
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rivka de Jongh
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Veronique A L Konijn
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Erik Mul
- Research Facilities, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Koos P J van Dam
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eileen W Stalman
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Boekel
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center location Reade, Amsterdam, The Netherlands
| | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center location Reade, Amsterdam, The Netherlands
| | - Sander W Tas
- Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Joep Killestein
- Department of Neurology, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Theo Rispens
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Neurophysiology, St Antonius Hospital, Nieuwegein, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Zoé L E van Kempen
- Department of Neurology, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - S Marieke van Ham
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anja Ten Brinke
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Carolien E van de Sandt
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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Leekha A, Saeedi A, Sefat KMSR, Kumar M, Martinez-Paniagua M, Damian A, Kulkarni R, Reichel K, Rezvan A, Masoumi S, Liu X, Cooper LJN, Sebastian M, Sands CM, Das VE, Patel NB, Hurst B, Varadarajan N. Multi-antigen intranasal vaccine protects against challenge with sarbecoviruses and prevents transmission in hamsters. Nat Commun 2024; 15:6193. [PMID: 39043645 PMCID: PMC11266618 DOI: 10.1038/s41467-024-50133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
Immunization programs against SARS-CoV-2 with commercial intramuscular vaccines prevent disease but are less efficient in preventing infections. Mucosal vaccines can provide improved protection against transmission, ideally for different variants of concern (VOCs) and related sarbecoviruses. Here, we report a multi-antigen, intranasal vaccine, NanoSTING-SN (NanoSTING-Spike-Nucleocapsid), eliminates virus replication in both the lungs and the nostrils upon challenge with the pathogenic SARS-CoV-2 Delta VOC. We further demonstrate that NanoSTING-SN prevents transmission of the SARS-CoV-2 Omicron VOC (BA.5) to vaccine-naïve hamsters. To evaluate protection against other sarbecoviruses, we immunized mice with NanoSTING-SN. We showed that immunization affords protection against SARS-CoV, leading to protection from weight loss and 100% survival in mice. In non-human primates, animals immunized with NanoSTING-SN show durable serum IgG responses (6 months) and nasal wash IgA responses cross-reactive to SARS-CoV-2 (XBB1.5), SARS-CoV and MERS-CoV antigens. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to reducing transmission of respiratory viruses, and (2) eliciting immunity against multiple antigens can be advantageous in engineering pan-sarbecovirus vaccines.
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Affiliation(s)
- Ankita Leekha
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - K M Samiur Rahman Sefat
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Monish Kumar
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Melisa Martinez-Paniagua
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Adrian Damian
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Rohan Kulkarni
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kate Reichel
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Ali Rezvan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Shalaleh Masoumi
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | | | | | | | - Vallabh E Das
- College of Optometry, University of Houston, Houston, TX, USA
| | - Nimesh B Patel
- College of Optometry, University of Houston, Houston, TX, USA
| | - Brett Hurst
- Institute of Antiviral Research, Utah State University, UT, Logan, USA
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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4
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Fan X, Song JW, Cao WJ, Zhou MJ, Yang T, Wang J, Meng FP, Shi M, Zhang C, Wang FS. T-Cell Epitope Mapping of SARS-CoV-2 Reveals Coordinated IFN-γ Production and Clonal Expansion of T Cells Facilitates Recovery from COVID-19. Viruses 2024; 16:1006. [PMID: 39066169 PMCID: PMC11281491 DOI: 10.3390/v16071006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND T-cell responses can be protective or detrimental during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, the underlying mechanism is poorly understood. METHODS In this study, we screened 144 15-mer peptides spanning the SARS-CoV-2 spike, nucleocapsid (NP), M, ORF8, ORF10, and ORF3a proteins and 39 reported SARS-CoV-1 peptides in peripheral blood mononuclear cells (PBMCs) from nine laboratory-confirmed coronavirus disease 2019 (COVID-19) patients (five moderate and four severe cases) and nine healthy donors (HDs) collected before the COVID-19 pandemic. T-cell responses were monitored by IFN-γ and IL-17A production using ELISA, and the positive samples were sequenced for the T cell receptor (TCR) β chain. The positive T-cell responses to individual SARS-CoV-2 peptides were validated by flow cytometry. RESULTS COVID-19 patients with moderate disease produced more IFN-γ than HDs and patients with severe disease (moderate vs. HDs, p < 0.0001; moderate vs. severe, p < 0.0001) but less IL-17A than those with severe disease (p < 0.0001). A positive correlation was observed between IFN-γ production and T-cell clonal expansion in patients with moderate COVID-19 (r = 0.3370, p = 0.0214) but not in those with severe COVID-19 (r = -0.1700, p = 0.2480). Using flow cytometry, we identified that a conserved peptide of the M protein (Peptide-120, P120) was a dominant epitope recognized by CD8+ T cells in patients with moderate disease. CONCLUSION Coordinated IFN-γ production and clonal expansion of SARS-CoV-2-specific T cells are associated with disease resolution in COVID-19. Our findings contribute to a better understanding of T-cell-mediated immunity in COVID-19 and may inform future strategies for managing and preventing severe outcomes of SARS-CoV-2 infection.
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Affiliation(s)
- Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Jin-Wen Song
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- Medical School of Chinese PLA, Beijing 100853, China
| | - Wen-Jing Cao
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Ming-Ju Zhou
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Tao Yang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Jing Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Fan-Ping Meng
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Ming Shi
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China; (X.F.); (J.-W.S.); (W.-J.C.); (M.-J.Z.); (T.Y.); (J.W.); (F.-P.M.); (M.S.)
- Medical School of Chinese PLA, Beijing 100853, China
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5
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Pierre CN, Adams LE, Higgins JS, Anasti K, Goodman D, Mielke D, Stanfield-Oakley S, Powers JM, Li D, Rountree W, Wang Y, Edwards RJ, Alam SM, Ferrari G, Tomaras GD, Haynes BF, Baric RS, Saunders KO. Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions. PLoS Pathog 2024; 20:e1011569. [PMID: 38900807 PMCID: PMC11218955 DOI: 10.1371/journal.ppat.1011569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 07/02/2024] [Accepted: 04/26/2024] [Indexed: 06/22/2024] Open
Abstract
Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non-neutralizing, yet it protected mice and cynomolgus macaques from severe disease. The mechanisms of NTD non-neutralizing antibody-mediated protection are unknown. Here we show that Fc effector functions mediate NTD non-neutralizing antibody (non-nAb) protection against SARS-CoV-2 MA10 viral challenge in mice. Though non-nAb prophylactic infusion did not suppress infectious viral titers in the lung as potently as neutralizing antibody (nAb) infusion, disease markers including gross lung discoloration were similar in nAb and non-nAb groups. Fc functional knockout substitutions abolished non-nAb protection and increased viral titers in the nAb group. Fc enhancement increased non-nAb protection relative to WT, supporting a positive association between Fc functionality and degree of protection from SARS-CoV-2 infection. For therapeutic administration of antibodies, non-nAb effector functions contributed to virus suppression and lessening of lung discoloration, but the presence of neutralization was required for optimal protection from disease. This study demonstrates that non-nAbs can utilize Fc-mediated mechanisms to lower viral load and prevent lung damage due to coronavirus infection.
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Affiliation(s)
- Camille N. Pierre
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lily E. Adams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jaclyn S. Higgins
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Derrick Goodman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Dieter Mielke
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sherry Stanfield-Oakley
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - John M. Powers
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
- Department of Immunology, Duke University, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University, Durham, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
- Department of Immunology, Duke University, Durham, North Carolina, United States of America
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6
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Garcia-Marquez MA, Thelen M, Bauer E, Maas L, Wennhold K, Lehmann J, Keller D, Nikolić M, George J, Zander T, Schröder W, Müller P, Yazbeck AM, Bruns C, Thomas R, Gathof B, Quaas A, Peifer M, Hillmer AM, von Bergwelt-Baildon M, Schlößer HA. Germline homozygosity and allelic imbalance of HLA-I are common in esophagogastric adenocarcinoma and impair the repertoire of immunogenic peptides. J Immunother Cancer 2024; 12:e007268. [PMID: 38631707 PMCID: PMC11029431 DOI: 10.1136/jitc-2023-007268] [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] [Accepted: 03/17/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The individual HLA-I genotype is associated with cancer, autoimmune diseases and infections. This study elucidates the role of germline homozygosity or allelic imbalance of HLA-I loci in esophago-gastric adenocarcinoma (EGA) and determines the resulting repertoires of potentially immunogenic peptides. METHODS HLA genotypes and sequences of either (1) 10 relevant tumor-associated antigens (TAAs) or (2) patient-specific mutation-associated neoantigens (MANAs) were used to predict good-affinity binders using an in silico approach for MHC-binding (www.iedb.org). Imbalanced or lost expression of HLA-I-A/B/C alleles was analyzed by transcriptome sequencing. FluoroSpot assays and TCR sequencing were used to determine peptide-specific T-cell responses. RESULTS We show that germline homozygosity of HLA-I genes is significantly enriched in EGA patients (n=80) compared with an HLA-matched reference cohort (n=7605). Whereas the overall mutational burden is similar, the repertoire of potentially immunogenic peptides derived from TAAs and MANAs was lower in homozygous patients. Promiscuity of peptides binding to different HLA-I molecules was low for most TAAs and MANAs and in silico modeling of the homozygous to a heterozygous HLA genotype revealed normalized peptide repertoires. Transcriptome sequencing showed imbalanced expression of HLA-I alleles in 75% of heterozygous patients. Out of these, 33% showed complete loss of heterozygosity, whereas 66% had altered expression of only one or two HLA-I molecules. In a FluoroSpot assay, we determined that peptide-specific T-cell responses against NY-ESO-1 are derived from multiple peptides, which often exclusively bind only one HLA-I allele. CONCLUSION The high frequency of germline homozygosity in EGA patients suggests reduced cancer immunosurveillance leading to an increased cancer risk. Therapeutic targeting of allelic imbalance of HLA-I molecules should be considered in EGA.
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Affiliation(s)
- Maria Alejandra Garcia-Marquez
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Martin Thelen
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Eugen Bauer
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Lukas Maas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Kerstin Wennhold
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Jonas Lehmann
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Diandra Keller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Miloš Nikolić
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Julie George
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Cologne, Cologne, Germany
| | - Thomas Zander
- Department I of Internal Medicine and Center for Integrated Oncology (CIO) Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | - Wolfgang Schröder
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Philipp Müller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Ali M Yazbeck
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Roman Thomas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Axel M Hillmer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Michael von Bergwelt-Baildon
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Gene Centre, Ludwig Maximilians University Munich, Munchen, Germany
- Department of Medicine III, Ludwig Maximilians University Munich, Munchen, Germany
| | - Hans Anton Schlößer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
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7
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Sheetikov SA, Khmelevskaya AA, Zornikova KV, Zvyagin IV, Shomuradova AS, Serdyuk YV, Shakirova NT, Peshkova IO, Titov A, Romaniuk DS, Shagina IA, Chudakov DM, Kiryukhin DO, Shcherbakova OV, Khamaganova EG, Dzutseva V, Afanasiev A, Bogolyubova AV, Efimov GA. Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein. Front Immunol 2024; 15:1369436. [PMID: 38629062 PMCID: PMC11018901 DOI: 10.3389/fimmu.2024.1369436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.
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Affiliation(s)
- Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra A. Khmelevskaya
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan V. Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alina S. Shomuradova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana V. Serdyuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Naina T. Shakirova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Iuliia O. Peshkova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Aleksei Titov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Dmitrii S. Romaniuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Irina A. Shagina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M. Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Dmitry O. Kiryukhin
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Olga V. Shcherbakova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ekaterina G. Khamaganova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Vitalina Dzutseva
- Novosibirsk State University, Medical School, Novosibirsk, Russia
- NPO Petrovax Pharm LLC, Moscow, Russia
| | | | | | - Grigory A. Efimov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
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8
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Tranter E, Frentsch M, Hütter-Krönke ML, Vuong GL, Busch D, Loyal L, Henze L, Rosnev S, Blau IW, Thiel A, Beule D, Bullinger L, Obermayer B, Na IK. Comparable CD8 + T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals. J Med Virol 2024; 96:e29539. [PMID: 38516755 DOI: 10.1002/jmv.29539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Despite extensive research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination responses in healthy individuals, there is comparatively little known beyond antibody titers and T-cell responses in the vulnerable cohort of patients after allogeneic hematopoietic stem cell transplantation (ASCT). In this study, we assessed the serological response and performed longitudinal multimodal analyses including T-cell functionality and single-cell RNA sequencing combined with T cell receptor (TCR)/B cell receptor (BCR) profiling in the context of BNT162b2 vaccination in ASCT patients. In addition, these data were compared to publicly available data sets of healthy vaccinees. Protective antibody titers were achieved in 40% of patients. We identified a distorted B- and T-cell distribution, a reduced TCR diversity, and increased levels of exhaustion marker expression as possible causes for the poorer vaccine response rates in ASCT patients. Immunoglobulin heavy chain gene rearrangement after vaccination proved to be highly variable in ASCT patients. Changes in TCRα and TCRβ gene rearrangement after vaccination differed from patterns observed in healthy vaccinees. Crucially, ASCT patients elicited comparable proportions of SARS-CoV-2 vaccine-induced (VI) CD8+ T-cells, characterized by a distinct gene expression pattern that is associated with SARS-CoV-2 specificity in healthy individuals. Our study underlines the impaired immune system and thus the lower vaccine response rates in ASCT patients. However, since protective vaccine responses and VI CD8+ T-cells can be induced in part of ASCT patients, our data advocate early posttransplant vaccination due to the high risk of infection in this vulnerable group.
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Affiliation(s)
- Eva Tranter
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Frentsch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marie Luise Hütter-Krönke
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giang Lam Vuong
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - David Busch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lucie Loyal
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Henze
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stanislav Rosnev
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Igor-Wolfgang Blau
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Thiel
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Bullinger
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Il-Kang Na
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
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9
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Pushpakumara PD, Jeewandara C, Bary F, Madushanka D, Perera L, Aberathna IS, Nimasha T, Jayamali J, Ranasinghe T, Kuruppu H, Danasekara S, Wijewickrama A, Ogg GS, Malavige GN. Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals. Clin Exp Immunol 2024; 215:268-278. [PMID: 37313783 PMCID: PMC10876109 DOI: 10.1093/cei/uxad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/25/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023] Open
Abstract
As there are limited data on B-cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron, and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n = 30), WT infected (n = 30), delta infected (n = 30), omicron infected + vaccinated (n = 20) and Sinopharm (BBIBP-CorV) vaccinees (n = 30). We then investigated the sensitivity and specificity of these immunodominant regions and analyzed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses, and bat Sarbecoviruses. We identified four immunodominant regions aa 29-52, aa 155-178, aa 274-297, and aa 365-388, which were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.
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Affiliation(s)
- Pradeep Darshana Pushpakumara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Farha Bary
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshan Madushanka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Lahiru Perera
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Inoka Sepali Aberathna
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thashmi Nimasha
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jeewantha Jayamali
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thushali Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Heshan Kuruppu
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Saubhagya Danasekara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Graham S Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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10
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Cankat S, Demael MU, Swadling L. In search of a pan-coronavirus vaccine: next-generation vaccine design and immune mechanisms. Cell Mol Immunol 2024; 21:103-118. [PMID: 38148330 PMCID: PMC10805787 DOI: 10.1038/s41423-023-01116-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Members of the coronaviridae family are endemic to human populations and have caused several epidemics and pandemics in recent history. In this review, we will discuss the feasibility of and progress toward the ultimate goal of creating a pan-coronavirus vaccine that can protect against infection and disease by all members of the coronavirus family. We will detail the unmet clinical need associated with the continued transmission of SARS-CoV-2, MERS-CoV and the four seasonal coronaviruses (HCoV-OC43, NL63, HKU1 and 229E) in humans and the potential for future zoonotic coronaviruses. We will highlight how first-generation SARS-CoV-2 vaccines and natural history studies have greatly increased our understanding of effective antiviral immunity to coronaviruses and have informed next-generation vaccine design. We will then consider the ideal properties of a pan-coronavirus vaccine and propose a blueprint for the type of immunity that may offer cross-protection. Finally, we will describe a subset of the diverse technologies and novel approaches being pursued with the goal of developing broadly or universally protective vaccines for coronaviruses.
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Affiliation(s)
- S Cankat
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK
| | - M U Demael
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK
| | - L Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK.
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11
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Rabdano S, Ruzanova E, Makarov D, Vertyachikh A, Teplykh V, Rudakov G, Pletyukhina I, Saveliev N, Zakharov K, Alpenidze D, Vasilyuk V, Arakelov S, Skvortsova V. Safety and Immunogenicity of the Convacell ® Recombinant N Protein COVID-19 Vaccine. Vaccines (Basel) 2024; 12:100. [PMID: 38276672 PMCID: PMC10821050 DOI: 10.3390/vaccines12010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
We have developed Convacell®-a COVID-19 vaccine based on the recombinant nucleocapsid (N) protein of SARS-CoV-2. This paper details Convacell's® combined phase I/II and IIb randomized, double-blind, interventional clinical trials. The primary endpoints were the frequency of adverse effects (AEs) and the titers of specific anti-N IgGs induced by the vaccination; secondary endpoints included the nature of the immune response. Convacell® demonstrated high safety in phase I with no severe AEs detected, 100% seroconversion by day 42 and high and sustained for 350 days anti-N IgG levels in phase II. Convacell® also demonstrated a fused cellular and humoral immune response. Phase IIb results showed significant post-vaccination increases in circulating anti-N IgG and N protein-specific IFNγ+-producing PBMC quantities among 438 volunteers. Convacell® showed same level of immunological efficacy for single and double dose vaccination regimens, including for elderly patients. The clinical studies indicate that Convacell® is safe and highly immunogenic.
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Affiliation(s)
- Sevastyan Rabdano
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Ellina Ruzanova
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Denis Makarov
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Anastasiya Vertyachikh
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Valeriya Teplykh
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - German Rudakov
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Iuliia Pletyukhina
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | - Nikita Saveliev
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
| | | | - Diana Alpenidze
- State Budgetary Health Institution “City Polyclinic No. 117”, St. Petersburg 194358, Russia
| | - Vasiliy Vasilyuk
- Department of Toxicology, Extreme and Diving Medicine, North-Western State Medical University named after I.I. Mechnikov, St. Petersburg 191015, Russia
| | - Sergei Arakelov
- Saint Petersburg Scientific Research Institute of Vaccines and Serums of the Federal Medical-Biological Agency of Russia (SPbSRIVS), St. Petersburg 198320, Russia (I.P.)
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12
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Wang Y, Yang L, Tang K, Zhang Y, Zhang C, Zhang Y, Jin B, Zhang Y, Zhuang R, Ma Y. Ad5-nCoV Vaccination Could Induce HLA-E Restricted CD8 + T Cell Responses Specific for Epitopes on Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein. Viruses 2023; 16:52. [PMID: 38257752 PMCID: PMC10820189 DOI: 10.3390/v16010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We evaluated cellular immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in an immunized population based on HLA-E-restricted CD8+ T cell epitope identification. HLA-E-restricted SARS-CoV-2 CD8+ T cell nonamer peptides were predicted with software. An HLA-E-transfected K562 cell binding assay was used to screen for high-affinity peptides. IFN-γ enzyme-linked immunospot assays were used to identify HLA-E-restricted epitopes. An HLA-E/epitope tetramer was employed to detect the frequencies of epitope-specific CD8+ T cells. Four CD8+ T cell epitopes on the spike protein of SARS-CoV-2 restricted by both HLA-E*0101 and E*0103 were identified. HLA-E-restricted epitope-specific IFN-γ-secreting CD8+ T cell responses could be detected in individuals vaccinated with SARS-CoV-2 vaccines. Importantly, the frequencies of epitope-specific CD8+ T cells in Ad5-nCoV vaccinated individuals were higher than in individuals vaccinated with recombinant protein or inactivated vaccines. Moreover, the frequencies of epitope-specific CD8+ T cells could be maintained for at least 120 days after only one dose of Ad5-nCoV vaccine, while the frequencies of epitope-specific CD8+ T cells decreased in individuals after two doses of Ad5-nCoV vaccine. These findings may contribute to a more comprehensive evaluation of the protective effects of vaccines for SARS-CoV-2; meanwhile, they may provide information to characterize HLA-E-restricted CD8+ T cell immunity against SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ran Zhuang
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
| | - Ying Ma
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
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13
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Esteban I, Pastor-Quiñones C, Usero L, Aurrecoechea E, Franceschini L, Esprit A, Gelpí JL, Martínez-Jiménez F, López-Bigas N, Breckpot K, Thielemans K, Leal L, Gómez CE, Sisteré-Oró M, Meyerhans A, Esteban M, Alonso MJ, García F, Plana M. Assessment of Human SARS CoV-2-Specific T-Cell Responses Elicited In Vitro by New Computationally Designed mRNA Immunogens (COVARNA). Vaccines (Basel) 2023; 12:15. [PMID: 38250827 PMCID: PMC10820377 DOI: 10.3390/vaccines12010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought significant changes and advances in the field of vaccination, including the implementation and widespread use of encapsidated mRNA vaccines in general healthcare practice. Here, we present two new mRNAs expressing antigenic parts of the SARS-CoV-2 spike protein and provide data supporting their functionality. The first mRNA, called RBD-mRNA, encodes a trimeric form of the virus spike protein receptor binding domain (RBD). The other mRNA, termed T-mRNA, codes for the relevant HLA I and II spike epitopes. The two mRNAs (COVARNA mRNAs) were designed to be used for delivery to cells in combination, with the RBD-mRNA being the primary source of antigen and the T-mRNA working as an enhancer of immunogenicity by supporting CD4 and CD8 T-cell activation. This innovative approach substantially differs from other available mRNA vaccines, which are largely directed to antibody production by the entire spike protein. In this study, we first show that both mRNAs are functionally transfected into human antigen-presenting cells (APCs). We obtained peripheral blood mononuclear cell (PBMC) samples from three groups of voluntary donors differing in their immunity against SARS-CoV-2: non-infected (naïve), infected-recovered (convalescent), and vaccinated. Using an established method of co-culturing autologous human dendritic cells (hDCs) with T-cells, we detected proliferation and cytokine secretion, thus demonstrating the ability of the COVARNA mRNAs to activate T-cells in an antigen-specific way. Interestingly, important differences in the intensity of the response between the infected-recovered (convalescent) and vaccinated donors were observed, with the levels of T-cell proliferation and cytokine secretion (IFNγ, IL-2R, and IL-13) being higher in the vaccinated group. In summary, our data support the further study of these mRNAs as a combined approach for future use as a vaccine.
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Affiliation(s)
- Ignasi Esteban
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Carmen Pastor-Quiñones
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Lorena Usero
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Elena Aurrecoechea
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Josep Lluís Gelpí
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, 08028 Barcelona, Spain;
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; (F.M.-J.); (N.L.-B.)
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; (F.M.-J.); (N.L.-B.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Lorna Leal
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Department of Infectious Diseases, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (C.E.G.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Marta Sisteré-Oró
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain;
| | - Andreas Meyerhans
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain;
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain;
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (C.E.G.); (M.E.)
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Felipe García
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Department of Infectious Diseases, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
| | - Montserrat Plana
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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14
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Fan J, Li S, Zhang Y, Zheng J, Wang D, Liao Y, Cui Z, Zhao D, Barouch DH, Yu J. Early Emerging SARS-CoV-2 Spike Mutants Are Diversified in Virologic Properties but Elicit Compromised Antibody Responses. Viruses 2023; 15:2401. [PMID: 38140642 PMCID: PMC10747620 DOI: 10.3390/v15122401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the effective antivirals and vaccines, COVID-19 remains a public health concern. The mutations that occurred during the early stage of the pandemic can be valuable in assessing the viral fitness and evolutionary trajectory. In this study, we analyzed a panel of 2969 spike sequences deposited in GISAID before April 2020 and characterized nine representative spike single-point mutants in detail. Compared with the WA01/2020, most (8 out of 9) mutants demonstrated an equivalent or diminished protein expression or processing, pseudovirus infectivity, and cell-cell fusion. Interestingly, most of the mutants in native form elicited minimum antibody responses in mice despite unaltered CD4+ and CD8+ T cell responses. The mutants remained sensitive to the antisera and the type I interferon. Taken together, these data suggest that the early emerging mutants are virologically divergent, and some of which showed transmission fitness. Our findings have important implications for the retrospective tracing of the early SARS-CoV-2 transmission and future pandemic preparedness.
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Affiliation(s)
- Junhao Fan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Shixiong Li
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yao Zhang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jihao Zheng
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Dongfang Wang
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
| | - Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhibo Cui
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (Y.L.); (D.Z.)
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China;
- Guangzhou National Laboratory, Bio-Island, Guangzhou 510005, China; (S.L.); (Y.Z.); (J.Z.); (D.W.); (Z.C.)
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15
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Yu H, Guan F, Miller H, Lei J, Liu C. The role of SARS-CoV-2 nucleocapsid protein in antiviral immunity and vaccine development. Emerg Microbes Infect 2023; 12:e2164219. [PMID: 36583642 PMCID: PMC9980416 DOI: 10.1080/22221751.2022.2164219] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ABSTRACTThe coronavirus disease 2019 (COVID-19) has caused enormous health risks and global economic disruption. This disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 nucleocapsid protein is a structural protein involved in viral replication and assembly. There is accumulating evidence indicating that the nucleocapsid protein is multi-functional, playing a key role in the pathogenesis of COVID-19 and antiviral immunity against SARS-CoV-2. Here, we summarize its potential application in the prevention of COVID-19, which is based on its role in inflammation, cell death, antiviral innate immunity, and antiviral adaptive immunity.
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Affiliation(s)
- Haiyun Yu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Heather Miller
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China, Chaohong Liu
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16
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Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
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Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
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17
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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18
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Leung D, Chan EYH, Mu X, Rosa Duque JS, Cheng SM, Ho FTW, Tong PC, Lai WM, Lee MH, Chim S, Tam IY, Tsang LC, Kwan KK, Chung Y, Wong HH, Lee AM, Li WY, Sze ST, Lam JH, Lee DH, Chan SM, Tu W, Peiris M, Ma ALT, Lau YL. Humoral and Cellular Immunogenicity of 3 Doses of BNT162b2 in Children With Kidney Diseases. Kidney Int Rep 2023; 8:2356-2367. [PMID: 38025215 PMCID: PMC10658278 DOI: 10.1016/j.ekir.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Patients with severe kidney diseases are at risk of complications from COVID-19; however, little is known about the effectiveness of COVID-19 vaccines in children and adolescents with kidney diseases. Methods We investigated the immunogenicity and safety of an accelerated 3-dose primary series of COVID-19 vaccination among 59 pediatric patients with chronic kidney disease (CKD) (mean age 12.9 years; 30 male) with or without immunosuppression, dialysis, or kidney transplant. Dosage was 0.1 ml BNT162b2 to those aged 5 to 11 years, and 0.3 ml BNT162b2 to those aged 11 to 18 years. Results Three doses of either vaccine type elicited significant antibody responses that included spike receptor-binding domain (S-RBD) IgG (90.5%-93.8% seropositive) and surrogate virus neutralization (geometric mean sVNT% level, 78.6%-79.3%). There were notable T cell responses. Weaker neutralization responses were observed among those on immunosuppression, especially those receiving higher number of immunosuppressants or on mycophenolate mofetil. Neutralization was reduced against Omicron BA.1 compared to wild type (WT, i.e., ancestral) (post-dose 3 sVNT% level; 82.7% vs. 27.4%; P < 0.0001). However, the T cell response against Omicron BA.1 was preserved, which likely confers protection against severe COVID-19. Infected patients exhibited hybrid immunity after vaccination, as evidenced by the higher Omicron BA.1 neutralization response among these infected patients who received 2 doses compared with those who were uninfected. Generally mild or moderate adverse reactions following vaccines were reported. Conclusion An accelerated 3-dose primary series with BNT162b2 is immunogenic and safe in young children and adolescents with kidney diseases.
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Affiliation(s)
- Daniel Leung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Eugene Yu-hin Chan
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Xiaofeng Mu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime S. Rosa Duque
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel M.S. Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Fanny Tsz-wai Ho
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Pak-chiu Tong
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Wai-ming Lai
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Matthew H.L. Lee
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Stella Chim
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Issan Y.S. Tam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo C.H. Tsang
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Kelvin K.H. Kwan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yuet Chung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Howard H.W. Wong
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Amos M.T. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wing Yan Li
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Summer T.K. Sze
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jennifer H.Y. Lam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Derek H.L. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Sau Man Chan
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wenwei Tu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection C2i, Hong Kong, China
| | - Alison Lap-tak Ma
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Yu Lung Lau
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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19
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Chen Q, Chia A, Hang SK, Lim A, Koh WK, Peng Y, Gao F, Chen J, Ho Z, Wai LE, Kunasegaran K, Tan AT, Le Bert N, Loh CY, Goh YS, Renia L, Dong T, Vathsala A, Bertoletti A. Engineering immunosuppressive drug-resistant armored (IDRA) SARS-CoV-2 T cells for cell therapy. Cell Mol Immunol 2023; 20:1300-1312. [PMID: 37666955 PMCID: PMC10616128 DOI: 10.1038/s41423-023-01080-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Solid organ transplant (SOT) recipients receive immunosuppressive drugs (ISDs) and are susceptible to developing severe COVID-19. Here, we analyze the Spike-specific T-cell response after 3 doses of mRNA vaccine in a group of SOT patients (n = 136) treated with different ISDs. We demonstrate that a combination of a calcineurin inhibitor (CNI), mycophenolate mofetil (MMF), and prednisone (Pred) treatment regimen strongly suppressed the mRNA vaccine-induced Spike-specific cellular response. Such defects have clinical consequences because the magnitude of vaccine-induced Spike-specific T cells was directly proportional to the ability of SOT patients to rapidly clear SARS-CoV-2 after breakthrough infection. To then compensate for the T-cell defects induced by immunosuppressive treatment and to develop an alternative therapeutic strategy for SOT patients, we describe production of 6 distinct SARS-CoV-2 epitope-specific ISD-resistant T-cell receptor (TCR)-T cells engineered using the mRNA electroporation method with reactivity minimally affected by mutations occurring in Beta, Delta, Gamma, and Omicron variants. This strategy with transient expression characteristics marks an improvement in the immunotherapeutic field and provides an attractive and novel therapeutic possibility for immunosuppressed COVID-19 patients.
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Affiliation(s)
- Qi Chen
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Adeline Chia
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Shou Kit Hang
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amy Lim
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Wee Kun Koh
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fei Gao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jili Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Zack Ho
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Lu-En Wai
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Kamini Kunasegaran
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Anthony Tanoto Tan
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nina Le Bert
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chiew Yee Loh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yun Shan Goh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Laurent Renia
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anantharaman Vathsala
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Antonio Bertoletti
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore.
- Singapore Immunology Network, A*STAR, Singapore, Singapore.
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20
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Kared H, Alirezaylavasani A, Lund KP, Chopra A, Tietze L, de Matos Kasahara T, Goll GL, Grødeland G, Kaarbø M, Reisæter AV, Hovd M, Heldal K, Vaage JT, Lund-Johansen F, Midtvedt K, Åsberg A, Munthe LA. Hybrid and SARS-CoV-2-vaccine immunity in kidney transplant recipients. EBioMedicine 2023; 97:104833. [PMID: 37844534 PMCID: PMC10585642 DOI: 10.1016/j.ebiom.2023.104833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Kidney transplant recipients (KTR) are at high risk for severe COVID-19 and have demonstrated poor response to vaccination, making it unclear whether successive vaccinations offer immunity and protection. METHODS We conducted a serologically guided interventional study where KTR patients that failed to seroconvert were revaccinated and also monitored seroconversion of KTR following the Norwegian vaccination program. We analysed IgG anti-RBD Spike responses from dose 2 (n = 432) up to after the 6th (n = 37) mRNA vaccine dose. The frequency and phenotype of Spike-specific T and B cell responses were assessed in the interventional cohort after 3-4 vaccine doses (n = 30). Additionally, we evaluated the Specific T and B cell response to breakthrough infection (n = 32), measured inflammatory cytokines and broadly cross-neutralizing antibodies, and defined the incidence of COVID-19-related hospitalizations and deaths. The Norwegian KTR cohort has a male dominance (2323 males, 1297 females), PBMC were collected from 114 male and 78 female donors. FINDINGS After vaccine dose 3, most KTR developed Spike-specific T cell responses but had significantly reduced Spike-binding B cells and few memory cells. The B cell response included a cross-reactive subset that could bind Omicron VOC, which expanded after breakthrough infection (BTI) and gave rise to a memory IgG+ B cell response. After BTI, KTR had increased Spike-specific T cells, emergent non-Spike T and B cell responses, and a systemic inflammatory signature. Late seroconversion occurred after doses 5-6, but 38% (14/37) of KTR had no detectable immunity even after multiple vaccine doses. INTERPRETATION Boosting vaccination can induce Spike-specific immunity that may expand in breakthrough infections highlighting the benefit of vaccination to protect this vulnerable population. FUNDING CEPI and internal funds.
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Affiliation(s)
- Hassen Kared
- KG Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway.
| | - Amin Alirezaylavasani
- KG Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Katrine Persgård Lund
- KG Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Adity Chopra
- Department of Immunology, Oslo University Hospital, Oslo, Norway; ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lisa Tietze
- Department of Immunology, Oslo University Hospital, Oslo, Norway; ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Guro Løvik Goll
- Division of Rheumatology and Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Gunnveig Grødeland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Mari Kaarbø
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Anna Varberg Reisæter
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Markus Hovd
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Kristian Heldal
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - John Torgils Vaage
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, Oslo, Norway; ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Karsten Midtvedt
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Anders Åsberg
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Norwegian Renal Registry, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ludvig A Munthe
- KG Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital, Oslo, Norway.
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21
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Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
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22
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Si Y, Wang Y, Tian Q, Wang Q, Pollard JM, Srivastava PK, Esser-Kahn AP, Collier JH, Sperling AI, Chong AS. Lung cDC1 and cDC2 dendritic cells priming naive CD8 + T cells in situ prior to migration to draining lymph nodes. Cell Rep 2023; 42:113299. [PMID: 37864794 PMCID: PMC10676754 DOI: 10.1016/j.celrep.2023.113299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/21/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
The current paradigm indicates that naive T cells are primed in secondary lymphoid organs. Here, we present evidence that intranasal administration of peptide antigens appended to nanofibers primes naive CD8+ T cells in the lung independently and prior to priming in the draining mediastinal lymph node (MLN). Notably, comparable accumulation and transcriptomic responses of CD8+ T cells in lung and MLN are observed in both Batf3KO and wild-type (WT) mice, indicating that, while cDC1 dendritic cells (DCs) are the major subset for cross-presentation, cDC2 DCs alone are capable of cross-priming CD8+ T cells both in the lung and draining MLN. Transcription analyses reveal distinct transcriptional responses in lung cDC1 and cDC2 to intranasal nanofiber immunization. However, both DC subsets acquire shared transcriptional responses upon migration into the lymph node, thus uncovering a stepwise activation process of cDC1 and cDC2 toward their ability to cross-prime effector and functional memory CD8+ T cell responses.
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Affiliation(s)
- Youhui Si
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Department of Surgery, The University of Chicago, Chicago, IL 60637, USA.
| | - Yihan Wang
- Department of Surgery, The University of Chicago, Chicago, IL 60637, USA
| | - Qiaomu Tian
- Department of Surgery, The University of Chicago, Chicago, IL 60637, USA
| | - Qiang Wang
- Department of Surgery, The University of Chicago, Chicago, IL 60637, USA
| | - Jared M Pollard
- Department of Surgery, The University of Chicago, Chicago, IL 60637, USA
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Aaron P Esser-Kahn
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
| | - Anne I Sperling
- Department of Medicine, Pulmonary and Critical Care, University of Virginia, Charlottesville, VA 22908, USA
| | - Anita S Chong
- Department of Surgery, The University of Chicago, Chicago, IL 60637, USA.
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23
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Soni MK, Migliori E, Fu J, Assal A, Chan HT, Pan J, Khatiwada P, Ciubotariu R, May MS, Pereira MR, De Giorgi V, Sykes M, Mapara MY, Muranski PJ. The prospect of universal coronavirus immunity: characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses. Front Immunol 2023; 14:1212203. [PMID: 37901229 PMCID: PMC10612330 DOI: 10.3389/fimmu.2023.1212203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
T cell immunity plays a central role in clinical outcomes of Coronavirus Infectious Disease 2019 (COVID-19) and T cell-focused vaccination or cellular immunotherapy might provide enhanced protection for some immunocompromised patients. Pre-existing T cell memory recognizing SARS-CoV-2 antigens antedating COVID-19 infection or vaccination, may have developed as an imprint of prior infections with endemic non-SARS human coronaviruses (hCoVs) OC43, HKU1, 229E, NL63, pathogens of "common cold". In turn, SARS-CoV-2-primed T cells may recognize emerging variants or other hCoV viruses and modulate the course of subsequent hCoV infections. Cross-immunity between hCoVs and SARS-CoV-2 has not been well characterized. Here, we systematically investigated T cell responses against the immunodominant SARS-CoV-2 spike, nucleocapsid and membrane proteins and corresponding antigens from α- and β-hCoVs among vaccinated, convalescent, and unexposed subjects. Broad T cell immunity against all tested SARS-CoV-2 antigens emerged in COVID-19 survivors. In convalescent and in vaccinated individuals, SARS-CoV-2 spike-specific T cells reliably recognized most SARS-CoV-2 variants, however cross-reactivity against the omicron variant was reduced by approximately 47%. Responses against spike, nucleocapsid and membrane antigens from endemic hCoVs were significantly more extensive in COVID-19 survivors than in unexposed subjects and displayed cross-reactivity between α- and β-hCoVs. In some, non-SARS hCoV-specific T cells demonstrated a prominent non-reciprocal cross-reactivity with SARS-CoV-2 antigens, whereas a distinct anti-SARS-CoV-2 immunological repertoire emerged post-COVID-19, with relatively limited cross-recognition of non-SARS hCoVs. Based on this cross-reactivity pattern, we established a strategy for in-vitro expansion of universal anti-hCoV T cells for adoptive immunotherapy. Overall, these results have implications for the future design of universal vaccines and cell-based immune therapies against SARS- and non-SARS-CoVs.
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Affiliation(s)
- Mithil K. Soni
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Edoardo Migliori
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Amer Assal
- Department of Medicine, Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY, United States
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Hei Ton Chan
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Jian Pan
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Prabesh Khatiwada
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Rodica Ciubotariu
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Michael S. May
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Marcus R. Pereira
- Department of Medicine, Division of Infectious Disease, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Valeria De Giorgi
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Markus Y. Mapara
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Pawel J. Muranski
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
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24
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Khadri L, Ziraksaz MH, Barekzai AB, Ghauri B. T cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 202:183-217. [PMID: 38237986 DOI: 10.1016/bs.pmbts.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a comprehensive analysis of T cell responses in COVID-19, focusing on T cell differentiation, specificity, and functional characteristics during SARS-CoV-2 infection. The differentiation of T cells in COVID-19 is explored, highlighting the key factors that influence T cell fate and effector functions. The immunology of the spike protein, a critical component of SARS-CoV-2, is discussed in detail, emphasizing its role in driving T-cell responses. The cellular immune responses against SARS-CoV-2 during acute infection are examined, including the specificity, phenotype, and functional attributes of SARS-CoV-2-specific T-cell responses. Furthermore, the chapter explores T-cell cross-recognition against other human coronaviruses (HCoVs) and the mechanisms of immune regulation mediated by spike proteins. This includes the induction of regulation through the innate immune system, the activation of self-spike protein-cross-reactive regulatory T cells, and the impact of self-tolerance on the regulation of spike proteins. The chapter investigates T cell responses to self-spike proteins and their implications in disease. The role of spike proteins as immunological targets in the context of COVID-19 is examined, shedding light on potential therapeutic interventions and clinical trials in autoimmune diseases. In conclusion, this chapter provides a comprehensive understanding of T cell responses in COVID-19, highlighting their differentiation, immune regulation, and clinical implications. This knowledge contributes to the development of targeted immunotherapies, vaccine strategies, and diagnostic approaches for COVID-19 and other related diseases.
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Affiliation(s)
- Laiqha Khadri
- Department of Biotechnology, Immune Inspired, Bangalore.
| | | | | | - Baber Ghauri
- Department of Biotechnology, Immune Inspired, Bangalore
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25
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Cao J, Gu H, Zhang X, Yun H, Li J, Si CY, Zhang J, Wang H. Intranasal inoculation of female BALB/c mice with replication-deficient human adenovirus type 5 expressing SARS-CoV-2 nucleocapsid protein aggravates lung pathology upon re-encountering the antigen. Virus Res 2023; 335:199201. [PMID: 37595663 PMCID: PMC10470087 DOI: 10.1016/j.virusres.2023.199201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Preclinical studies indicate that SARS-CoV-2 nucleocapsid (N)-based vaccines, along with other viral protein(s), confer protection in various animal models against infection by SARS-CoV-2 ancestral virus and variants of concern. However, the optimal vaccination procedure and the role of N-specific host adaptive immune responses remain elusive. Here, we report that intranasal inoculation with replication-deficient human adenovirus type 5 expressing SARS-CoV-2 N protein (Ad5-N) conferred no protection in the lung of female BALB/c mice upon re-encountering the antigen, either by 10-fold Ad5-N re-exposure or sublethal infection of mouse-adapted SARS-CoV-2. By contrast, this procedure led to aggravated lung pathology with more necroptotic CD3+ T cells and Ly6G+ granulocytes, which was associated with the accumulation of IFN-γ-expressing antigen-experienced CD4+ and CD8+ T cells. These findings pre-caution the clinical application of this vaccination procedure. Furthermore, our data suggest that excessive host adaptive immune responses against N protein contributes to COVID-19 pathogenesis.
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Affiliation(s)
- Junxia Cao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hongjing Gu
- Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xueting Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hongfang Yun
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jiarong Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; University of South China, Hengyang Medical School, Hengyang 421001, China
| | - Chuan-Yimu Si
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jiyan Zhang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China; University of South China, Hengyang Medical School, Hengyang 421001, China; Anhui Medical University, Hefei 230032, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Hui Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
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26
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Andrade AGD, Comberlang FC, Cavalcante-Silva LHA, Kessen TSL. COVID-19 vaccination: Effects of immunodominant peptides of SARS-CoV-2. Cytokine 2023; 170:156339. [PMID: 37607411 DOI: 10.1016/j.cyto.2023.156339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023]
Abstract
T-cell immunity plays a critical role in controlling viral infections, making it essential to identify specific viral targets to develop effective vaccines. In this study, we focused on identifying and understanding the potential effects of different SARS-CoV-2-derived peptides, including spike, nucleocapsid, and ORFs, that have the potential to serve as T-cell epitopes. Assessing T cell response through flow cytometry, we demonstrated that PBMC collected from vaccinated individuals had a significantly higher expression of important biomarkers in controlling viral infection and proper regulation of immune response mediated by T CD4+ and T CD8+ cells stimulated with immunodominant peptides. These data highlight how cellular immune responses to some of these peptides could contribute to SARS-CoV-2 protection due to COVID-19 immunization.
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Affiliation(s)
- Arthur Gomes de Andrade
- Immunology of Infectious Diseases Laboratory, Department of Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil
| | - Fernando Cézar Comberlang
- Immunology of Infectious Diseases Laboratory, Department of Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil
| | - Luiz Henrique Agra Cavalcante-Silva
- Immunology of Infectious Diseases Laboratory, Department of Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil
| | - Tatjana Souza Lima Kessen
- Immunology of Infectious Diseases Laboratory, Department of Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil.
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27
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Antoun E, Peng Y, Dong T. Vaccine-induced CD8 + T cells are key to protection from SARS-CoV-2. Nat Immunol 2023; 24:1594-1596. [PMID: 37735590 DOI: 10.1038/s41590-023-01621-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Affiliation(s)
- Elie Antoun
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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28
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Chiuppesi F, Ortega-Francisco S, Gutierrez MA, Li J, Ly M, Faircloth K, Mack-Onyeike J, La Rosa C, Thomas S, Zhou Q, Drake J, Slape C, Fernando P, Rida W, Kaltcheva T, Grifoni A, Sette A, Patterson A, Dempsey S, Ball B, Ali H, Salhotra A, Stein A, Nathwani N, Rosenzweig M, Nikolaenko L, Al Malki MM, Dickter J, Nanayakkara DD, Puing A, Forman SJ, Taplitz RA, Zaia JA, Nakamura R, Wussow F, Diamond DJ, Dadwal SS. Stimulation of Potent Humoral and Cellular Immunity via Synthetic Dual-Antigen MVA-Based COVID-19 Vaccine COH04S1 in Cancer Patients Post Hematopoietic Cell Transplantation and Cellular Therapy. Vaccines (Basel) 2023; 11:1492. [PMID: 37766168 PMCID: PMC10538048 DOI: 10.3390/vaccines11091492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Hematopoietic cell transplantation (HCT) and chimeric antigen receptor (CAR)-T cell patients are immunocompromised, remain at high risk following SARS-CoV-2 infection, and are less likely than immunocompetent individuals to respond to vaccination. As part of the safety lead-in portion of a phase 2 clinical trial in patients post HCT/CAR-T for hematological malignancies (HM), we tested the immunogenicity of the synthetic modified vaccinia Ankara-based COVID-19 vaccine COH04S1 co-expressing spike (S) and nucleocapsid (N) antigens. Thirteen patients were vaccinated 3-12 months post HCT/CAR-T with two to four doses of COH04S1. SARS-CoV-2 antigen-specific humoral and cellular immune responses, including neutralizing antibodies to ancestral virus and variants of concern (VOC), were measured up to six months post vaccination and compared to immune responses in historical cohorts of naïve healthy volunteers (HV) vaccinated with COH04S1 and naïve healthcare workers (HCW) vaccinated with the FDA-approved mRNA vaccine Comirnaty® (Pfizer, New York, NY, USA). After one or two COH04S1 vaccine doses, HCT/CAR-T recipients showed a significant increase in S- and N-specific binding antibody titers and neutralizing antibodies with potent activity against SARS-CoV-2 ancestral virus and VOC, including the highly immune evasive Omicron XBB.1.5 variant. Furthermore, vaccination with COH04S1 resulted in a significant increase in S- and N-specific T cells, predominantly CD4+ T lymphocytes. Elevated S- and N-specific immune responses continued to persist at six months post vaccination. Furthermore, both humoral and cellular immune responses in COH04S1-vaccinated HCT/CAR-T patients were superior or comparable to those measured in COH04S1-vaccinated HV or Comirnaty®-vaccinated HCW. These results demonstrate robust stimulation of SARS-CoV-2 S- and N-specific immune responses including cross-reactive neutralizing antibodies by COH04S1 in HM patients post HCT/CAR-T, supporting further testing of COH04S1 in immunocompromised populations.
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Affiliation(s)
- Flavia Chiuppesi
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Sandra Ortega-Francisco
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Miguel-Angel Gutierrez
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Jing Li
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Minh Ly
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Katelyn Faircloth
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Jada Mack-Onyeike
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Corinna La Rosa
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Sandra Thomas
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Qiao Zhou
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Jennifer Drake
- Clinical Trials Office, City of Hope National Medical Center, Duarte, CA 91010, USA; (J.D.); (C.S.); (P.F.)
| | - Cynthia Slape
- Clinical Trials Office, City of Hope National Medical Center, Duarte, CA 91010, USA; (J.D.); (C.S.); (P.F.)
| | - Paolo Fernando
- Clinical Trials Office, City of Hope National Medical Center, Duarte, CA 91010, USA; (J.D.); (C.S.); (P.F.)
| | - Wasima Rida
- Independent Researcher, Arlington, VA 22205, USA;
| | - Teodora Kaltcheva
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology, University of California San Diego, La Jolla, CA 92037, USA; (A.G.); (A.S.)
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology, University of California San Diego, La Jolla, CA 92037, USA; (A.G.); (A.S.)
| | - Angela Patterson
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Shannon Dempsey
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Brian Ball
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Haris Ali
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Amandeep Salhotra
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Anthony Stein
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Nitya Nathwani
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Michael Rosenzweig
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Liana Nikolaenko
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Monzr M. Al Malki
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Jana Dickter
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Deepa D. Nanayakkara
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Alfredo Puing
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Stephen J. Forman
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Randy A. Taplitz
- Division of Infectious Diseases, City of Hope National Medical Center, Duarte, CA 91010, USA; (R.A.T.); (S.S.D.)
- Department of Medicine, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - John A. Zaia
- Center for Gene Therapy, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Ryotaro Nakamura
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Felix Wussow
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Don J. Diamond
- Department of Hematology and HCT, Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; (F.C.); (S.O.-F.); (M.-A.G.); (J.L.); (K.F.); (J.M.-O.); (C.L.R.); (S.T.); (Q.Z.); (T.K.); (A.P.); (S.D.); (B.B.); (H.A.); (A.S.); (A.S.); (N.N.); (M.R.); (L.N.); (M.M.A.M.); (J.D.); (D.D.N.); (S.J.F.); (R.N.); (F.W.)
| | - Sanjeet S. Dadwal
- Division of Infectious Diseases, City of Hope National Medical Center, Duarte, CA 91010, USA; (R.A.T.); (S.S.D.)
- Department of Medicine, City of Hope National Medical Center, Duarte, CA 91010, USA
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Ferrantelli F, Manfredi F, Chiozzini C, Leone P, Pugliese K, Spada M, Di Virgilio A, Giovannelli A, Valeri M, Cara A, Michelini Z, Andreotti M, Federico M. SARS-CoV-2-Specific CD8 + T-Cells in Blood but Not in the Lungs of Vaccinated K18-hACE2 Mice after Infection. Vaccines (Basel) 2023; 11:1433. [PMID: 37766110 PMCID: PMC10535545 DOI: 10.3390/vaccines11091433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 enters the host by infecting nasal ciliated cells. Then, the virus can spread towards the oropharyngeal cavity and the pulmonary tissues. The antiviral adaptive immunity is promptly induced in response to the virus's detection, with virus-specific T-lymphocytes appearing before antiviral antibodies. Both the breadth and potency of antiviral CD8+ T-cell immunity have a key role in containing viral spread and disease severity. Current anti-SARS-CoV-2 vaccines do not impede the virus's replication in the upper respiratory tract, and there is consensus on the fact that the best potency of the antiviral immune response in both blood and the upper respiratory tract can be reached upon infection in vaccinees (i.e., breakthrough infection). However, whether the antiviral CD8+ T-cells developing in response to the breakthrough infection in the upper respiratory tract diffuse to the lungs is also still largely unknown. To fill the gap, we checked the CD8+ T-cell immunity elicited after infection of K18-hACE2 transgenic mice both at 3 weeks and 3 months after anti-spike vaccination. Virus-specific CD8+ T-cell immunity was monitored in both blood and the lungs before and after infection. By investigating the de novo generation of the CD8+ T-cells specific for SARS-CoV-2 viral proteins, we found that both membrane (M) and/or nucleocapsid (N)-specific CD8+ T-cells were induced at comparable levels in the blood of both unvaccinated and vaccinated mice. Conversely, N-specific CD8+ T-cells were readily found in the lungs of the control mice but were either rare or absent in those of vaccinated mice. These results support the idea that the hybrid cell immunity developing after asymptomatic/mild breakthrough infection strengthens the antiviral cell immunity in the lungs only marginally, implying that the direct exposition of viral antigens is required for the induction of an efficient antiviral cell immunity in the lungs.
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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.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Francesco Manfredi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Chiara Chiozzini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Patrizia Leone
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Katherina Pugliese
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Massimo Spada
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Antonio Di Virgilio
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Andrea Giovannelli
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Mauro Valeri
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (A.D.V.); (A.G.); (M.V.)
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
| | - Maurizio Federico
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (F.M.); (C.C.); (P.L.); (K.P.); (A.C.); (Z.M.); (M.A.)
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Song W, Fang Z, Ma F, Li J, Huang Z, Zhang Y, Li J, Chen K. The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: present status and prospects. Front Microbiol 2023; 14:1217567. [PMID: 37675423 PMCID: PMC10478715 DOI: 10.3389/fmicb.2023.1217567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Despite many countries rapidly revising their strategies to prevent contagions, the number of people infected with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to surge. The emergent variants that can evade the immune response significantly affect the effectiveness of mainstream vaccines and diagnostic products based on the original spike protein. Therefore, it is essential to focus on the highly conserved nature of the nucleocapsid protein as a potential target in the field of vaccines and diagnostics. In this regard, our review initially discusses the structure, function, and mechanism of action of N protein. Based on this discussion, we summarize the relevant research on the in-depth development and application of diagnostic methods and vaccines based on N protein, such as serology and nucleic acid detection. Such valuable information can aid in designing more efficient diagnostic and vaccine tools that could help end the SARS-CoV-2 pandemic.
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Affiliation(s)
- Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Feike Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanjun Zhang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianhua Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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31
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Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023; 620:128-136. [PMID: 37468623 PMCID: PMC10396966 DOI: 10.1038/s41586-023-06331-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lawton D Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Noah D Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karoline Guthrie
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Victoria W Murray
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gurjot S Gill
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Colin T Maguire
- Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Cynthia A Vierra-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | - Michael J Dewar-Oldis
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sulggi Lee
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gregory M Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey E Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Division of General Internal Medicine, University of California, San Francisco, CA, USA
| | - Martin Maiers
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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32
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Hertz T, Levy S, Ostrovsky D, Oppenheimer H, Zismanov S, Kuzmina A, Friedman LM, Trifkovic S, Brice D, Chun-Yang L, Cohen-Lavi L, Shemer-Avni Y, Cohen-Lahav M, Amichay D, Keren-Naus A, Voloshin O, Weber G, Najjar-Debbiny R, Chazan B, McGargill MA, Webby R, Chowers M, Novack L, Novack V, Taube R, Nesher L, Weinstein O. Correlates of protection for booster doses of the SARS-CoV-2 vaccine BNT162b2. Nat Commun 2023; 14:4575. [PMID: 37516771 PMCID: PMC10387073 DOI: 10.1038/s41467-023-39816-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/28/2023] [Indexed: 07/31/2023] Open
Abstract
Vaccination, especially with multiple doses, provides substantial population-level protection against COVID-19, but emerging variants of concern (VOC) and waning immunity represent significant risks at the individual level. Here we identify correlates of protection (COP) in a multicenter prospective study following 607 healthy individuals who received three doses of the Pfizer-BNT162b2 vaccine approximately six months prior to enrollment. We compared 242 individuals who received a fourth dose to 365 who did not. Within 90 days of enrollment, 239 individuals contracted COVID-19, 45% of the 3-dose group and 30% of the four-dose group. The fourth dose elicited a significant rise in antibody binding and neutralizing titers against multiple VOCs reducing the risk of symptomatic infection by 37% [95%CI, 15%-54%]. However, a group of individuals, characterized by low baseline titers of binding antibodies, remained susceptible to infection despite significantly increased neutralizing antibody titers upon boosting. A combination of reduced IgG levels to RBD mutants and reduced VOC-recognizing IgA antibodies represented the strongest COP in both the 3-dose group (HR = 6.34, p = 0.008) and four-dose group (HR = 8.14, p = 0.018). We validated our findings in an independent second cohort. In summary combination IgA and IgG baseline binding antibody levels may identify individuals most at risk from future infections.
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Affiliation(s)
- Tomer Hertz
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, USA.
| | - Shlomia Levy
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Ostrovsky
- Clinical Research Center, Soroka University Medical Center, and the faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hanna Oppenheimer
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shosh Zismanov
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alona Kuzmina
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M Friedman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sanja Trifkovic
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Brice
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lin Chun-Yang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liel Cohen-Lavi
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonat Shemer-Avni
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Laboratory of Virology, Soroka University Medical Center, Beer-Sheva, Israel
| | - Merav Cohen-Lahav
- Laboratory of Management, Soroka University Medical Center, Beer-Sheva, Israel
| | - Doron Amichay
- Central Laboratory, Clalit Health Services & Dept. of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Ayelet Keren-Naus
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Laboratory of Virology, Soroka University Medical Center, Beer-Sheva, Israel
| | - Olga Voloshin
- Laboratory of Virology, Soroka University Medical Center, Beer-Sheva, Israel
| | - Gabriel Weber
- Infectious Diseases Unit, Lady Davis Carmel Medical Center, Haifa, Israel
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ronza Najjar-Debbiny
- Infectious Diseases Unit, Lady Davis Carmel Medical Center, Haifa, Israel
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Bibiana Chazan
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Infectious Diseases Unit, Emek Medical Center, Afula, Israel
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michal Chowers
- School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Meir Medical Center, Kfar Saba, Israel
| | - Lena Novack
- Clinical Research Center, Soroka University Medical Center, and the faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Victor Novack
- Clinical Research Center, Soroka University Medical Center, and the faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ran Taube
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Lior Nesher
- Infectious Disease Institute, Soroka University Medical Center, and Faculty of Health Sciences, Ben-Gurion University, Beer Sheba, Israel.
| | - Orly Weinstein
- Dept. of Health systems management, faculty of health sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Hospital division, Clalit Health Services, Tel Aviv, Israel
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Jiang N, Malone M, Chizari S. Antigen-specific and cross-reactive T cells in protection and disease. Immunol Rev 2023; 316:120-135. [PMID: 37209375 PMCID: PMC10524458 DOI: 10.1111/imr.13217] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Human T cells have a diverse T-cell receptor (TCR) repertoire that endows them with the ability to identify and defend against a broad spectrum of antigens. The universe of possible antigens that T cells may encounter, however, is even larger. To effectively surveil such a vast universe, the T-cell repertoire must adopt a high degree of cross-reactivity. Likewise, antigen-specific and cross-reactive T-cell responses play pivotal roles in both protective and pathological immune responses in numerous diseases. In this review, we explore the implications of these antigen-driven T-cell responses, with a particular focus on CD8+ T cells, using infection, neurodegeneration, and cancer as examples. We also summarize recent technological advances that facilitate high-throughput profiling of antigen-specific and cross-reactive T-cell responses experimentally, as well as computational biology approaches that predict these interactions.
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Affiliation(s)
- Ning Jiang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, 19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Shahab Chizari
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
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Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Canto Gomes J, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Sci Immunol 2023; 8:eabl8881. [PMID: 37390223 DOI: 10.1126/sciimmunol.abl8881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Pathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E-restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E peptide-specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E-restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells.
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Affiliation(s)
- Hongbing Yang
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Hong Sun
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lucy Walters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lee Garner
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona Moore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bas W A Peeters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
| | - Joao Canto Gomes
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Ana Tomas
- Unidada de Investigacao em Patobiologia Molecular, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, EPE Lisbon, Portugal
- Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Unit, Alder Hey Children's Hospital, Eaton Road, Liverpool L12 2AP, UK
| | - Lance C W Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | | | | | - Alexander J Mentzer
- Welcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
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35
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Primard C, Monchâtre-Leroy E, Del Campo J, Valsesia S, Nikly E, Chevandier M, Boué F, Servat A, Wasniewski M, Picard-Meyer E, Courant T, Collin N, Salguero FJ, Le Vert A, Guyon-Gellin D, Nicolas F. OVX033, a nucleocapsid-based vaccine candidate, provides broad-spectrum protection against SARS-CoV-2 variants in a hamster challenge model. Front Immunol 2023; 14:1188605. [PMID: 37409116 PMCID: PMC10319154 DOI: 10.3389/fimmu.2023.1188605] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Spike-based COVID-19 vaccines induce potent neutralizing antibodies but their efficacy against SARS-CoV-2 variants decreases. OVX033 is a recombinant protein composed of the full-length nucleocapsid (N) protein of SARS-CoV-2 genetically fused to oligoDOM®, a self-assembling domain which improves antigen immunogenicity. OVX033 including N as an antigenic target is proposed as new vaccine candidate providing broad-spectrum protection against sarbecoviruses. OVX033 demonstrated its ability to trigger cross-reactive T cell responses and cross-protection against three variants of SARS-CoV-2 (B.1 Europe, Delta B.1.617.2, and Omicron B.1.1.529) in a hamster challenge model, as evidenced by lower weight loss, lower lung viral loads, and reduced lung histopathological lesions.
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Affiliation(s)
| | | | | | | | | | | | - Franck Boué
- ANSES, Laboratory for Rabies and Wildlife, Malzéville, France
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Milighetti M, Peng Y, Tan C, Mark M, Nageswaran G, Byrne S, Ronel T, Peacock T, Mayer A, Chandran A, Rosenheim J, Whelan M, Yao X, Liu G, Felce SL, Dong T, Mentzer AJ, Knight JC, Balloux F, Greenstein E, Reich-Zeliger S, Pade C, Gibbons JM, Semper A, Brooks T, Otter A, Altmann DM, Boyton RJ, Maini MK, McKnight A, Manisty C, Treibel TA, Moon JC, Noursadeghi M, Chain B. Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection. iScience 2023; 26:106937. [PMID: 37275518 PMCID: PMC10201888 DOI: 10.1016/j.isci.2023.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/14/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023] Open
Abstract
T cell responses precede antibody and may provide early control of infection. We analyzed the clonal basis of this rapid response following SARS-COV-2 infection. We applied T cell receptor (TCR) sequencing to define the trajectories of individual T cell clones immediately. In SARS-COV-2 PCR+ individuals, a wave of TCRs strongly but transiently expand, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains but not with circulating human coronaviruses. Many expanding CDR3s were present at high frequency in pre-pandemic repertoires. Early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the preinfection naive repertoire. High-frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michal Mark
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gayathri Nageswaran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Suzanne Byrne
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Tom Peacock
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Xuan Yao
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | | | - Julian C Knight
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Erez Greenstein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shlomit Reich-Zeliger
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Amanda Semper
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Tim Brooks
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Ashley Otter
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London SW7 2BX, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Lung Division, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Aine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - Charlotte Manisty
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Thomas A Treibel
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - James C Moon
- Institute of Cardiovascular Sciences, University College London, London WC1E 6BT, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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37
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Visvabharathy L, Hanson BA, Orban ZS, Lim PH, Palacio NM, Jimenez M, Clark JR, Graham EL, Liotta EM, Tachas G, Penaloza-MacMaster P, Koralnik IJ. Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein. Front Immunol 2023; 14:1155770. [PMID: 37313412 PMCID: PMC10258318 DOI: 10.3389/fimmu.2023.1155770] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/11/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction Many people with long COVID symptoms suffer from debilitating neurologic post-acute sequelae of SARS-CoV-2 infection (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether PASC symptoms impact virus-specific immune responses. Therefore, we examined T cell and antibody responses to SARS-CoV-2 Nucleocapsid protein to identify activation signatures distinguishing Neuro-PASC patients from healthy COVID convalescents. Results We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated CD4+ T cell responses and diminished CD8+ memory T cell activation toward the C-terminal region of SARS-CoV-2 Nucleocapsid protein when examined both functionally and using TCR sequencing. CD8+ T cell production of IL-6 correlated with increased plasma IL-6 levels as well as heightened severity of neurologic symptoms, including pain. Elevated plasma immunoregulatory and reduced pro-inflammatory and antiviral response signatures were evident in Neuro-PASC patients compared with COVID convalescent controls without lasting symptoms, correlating with worse neurocognitive dysfunction. Discussion We conclude that these data provide new insight into the impact of virus-specific cellular immunity on the pathogenesis of long COVID and pave the way for the rational design of predictive biomarkers and therapeutic interventions.
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Affiliation(s)
- Lavanya Visvabharathy
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Barbara A. Hanson
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Zachary S. Orban
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Patrick H. Lim
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Nicole M. Palacio
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Millenia Jimenez
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jeffrey R. Clark
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Edith L. Graham
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Eric M. Liotta
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - George Tachas
- Drug Discovery & Patents, Antisense Therapeutics Ltd., Melbourne, VIC, Australia
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Igor J. Koralnik
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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Eser TM, Baranov O, Huth M, Ahmed MIM, Deák F, Held K, Lin L, Pekayvaz K, Leunig A, Nicolai L, Pollakis G, Buggert M, Price DA, Rubio-Acero R, Reich J, Falk P, Markgraf A, Puchinger K, Castelletti N, Olbrich L, Vanshylla K, Klein F, Wieser A, Hasenauer J, Kroidl I, Hoelscher M, Geldmacher C. Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion. Nat Commun 2023; 14:2952. [PMID: 37225706 DOI: 10.1038/s41467-023-38020-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 05/26/2023] Open
Abstract
Despite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19.
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Affiliation(s)
- Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Manuel Huth
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
| | - Mohammed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Luming Lin
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Alexander Leunig
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE, UK
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Jakob Reich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Philine Falk
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Alissa Markgraf
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Kerstin Puchinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, LMU Munich, 81377, Munich, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, 53113, Bonn, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany.
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39
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Wing PAC, Schmidt NM, Peters R, Erdmann M, Brown R, Wang H, Swadling L, Newman J, Thakur N, Shionoya K, Morgan SB, Hinks TSC, Watashi K, Bailey D, Hansen SB, Davidson AD, Maini MK, McKeating JA. An ACAT inhibitor suppresses SARS-CoV-2 replication and boosts antiviral T cell activity. PLoS Pathog 2023; 19:e1011323. [PMID: 37134108 PMCID: PMC10202285 DOI: 10.1371/journal.ppat.1011323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 05/22/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
The severity of disease following infection with SARS-CoV-2 is determined by viral replication kinetics and host immunity, with early T cell responses and/or suppression of viraemia driving a favourable outcome. Recent studies uncovered a role for cholesterol metabolism in the SARS-CoV-2 life cycle and in T cell function. Here we show that blockade of the enzyme Acyl-CoA:cholesterol acyltransferase (ACAT) with Avasimibe inhibits SARS-CoV-2 pseudoparticle infection and disrupts the association of ACE2 and GM1 lipid rafts on the cell membrane, perturbing viral attachment. Imaging SARS-CoV-2 RNAs at the single cell level using a viral replicon model identifies the capacity of Avasimibe to limit the establishment of replication complexes required for RNA replication. Genetic studies to transiently silence or overexpress ACAT isoforms confirmed a role for ACAT in SARS-CoV-2 infection. Furthermore, Avasimibe boosts the expansion of functional SARS-CoV-2-specific T cells from the blood of patients sampled during the acute phase of infection. Thus, re-purposing of ACAT inhibitors provides a compelling therapeutic strategy for the treatment of COVID-19 to achieve both antiviral and immunomodulatory effects. Trial registration: NCT04318314.
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Affiliation(s)
- Peter A. C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nathalie M. Schmidt
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | - Rory Peters
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maximilian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Rachel Brown
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
- UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Hao Wang
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, San Diego, California, United States of America
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, San Diego, California, United States of America
| | - Leo Swadling
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | | | | | | | - Kaho Shionoya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Research Centre for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sophie B. Morgan
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy SC Hinks
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Research Centre for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Scott B. Hansen
- UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mala K. Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | - Jane A. McKeating
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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40
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Tani Y, Takita M, Kobashi Y, Wakui M, Zhao T, Yamamoto C, Saito H, Kawashima M, Sugiura S, Nishikawa Y, Omata F, Shimazu Y, Kawamura T, Sugiyama A, Nakayama A, Kaneko Y, Kodama T, Kami M, Tsubokura M. Varying Cellular Immune Response against SARS-CoV-2 after the Booster Vaccination: A Cohort Study from Fukushima Vaccination Community Survey, Japan. Vaccines (Basel) 2023; 11:vaccines11050920. [PMID: 37243024 DOI: 10.3390/vaccines11050920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Booster vaccination reduces the incidence of severe cases and mortality related to COVID-19, with cellular immunity playing an important role. However, little is known about the proportion of the population that has achieved cellular immunity after booster vaccination. Thus, we conducted a Fukushima cohort database and assessed humoral and cellular immunity in 2526 residents and healthcare workers in Fukushima Prefecture in Japan through continuous blood collection every 3 months from September 2021. We identified the proportion of people with induced cellular immunity after booster vaccination using the T-SPOT.COVID test, and analyzed their background characteristics. Among 1089 participants, 64.3% (700/1089) had reactive cellular immunity after booster vaccination. Multivariable analysis revealed the following independent predictors of reactive cellular immunity: age < 40 years (adjusted odds ratio: 1.81; 95% confidence interval: 1.19-2.75; p-value: 0.005) and adverse reactions after vaccination (1.92, 1.19-3.09, 0.007). Notably, despite IgG(S) and neutralizing antibody titers of ≥500 AU/mL, 33.9% (349/1031) and 33.5% (341/1017) of participants, respectively, did not have reactive cellular immunity. In summary, this is the first study to evaluate cellular immunity at the population level after booster vaccination using the T-SPOT.COVID test, albeit with several limitations. Future studies will need to evaluate previously infected subjects and their T-cell subsets.
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Affiliation(s)
- Yuta Tani
- Medical Governance Research Institute, Tokyo 108-0074, Japan
| | - Morihito Takita
- Medical Governance Research Institute, Tokyo 108-0074, Japan
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Yurie Kobashi
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima 963-8202, Japan
| | - Masatoshi Wakui
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Tianchen Zhao
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Chika Yamamoto
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Hiroaki Saito
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
- Department of Internal Medicine, Soma Central Hospital, Fukushima 976-0016, Japan
| | - Moe Kawashima
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Sota Sugiura
- Medical Governance Research Institute, Tokyo 108-0074, Japan
| | - Yoshitaka Nishikawa
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima 963-8202, Japan
| | - Fumiya Omata
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima 963-8202, Japan
| | - Yuzo Shimazu
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima 963-8202, Japan
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Akira Sugiyama
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Aya Nakayama
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yudai Kaneko
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Medical and Biological Laboratories Co., Ltd., Tokyo 105-0012, Japan
| | - Tetsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Masahiro Kami
- Medical Governance Research Institute, Tokyo 108-0074, Japan
| | - Masaharu Tsubokura
- Department of Radiation Health Management, Fukushima Medical University, Fukushima 960-1295, Japan
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima 963-8202, Japan
- Department of Internal Medicine, Soma Central Hospital, Fukushima 976-0016, Japan
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41
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Gómez de la Torre JC, Hueda-Zavaleta M, Cáceres-DelAguila JA, Muro-Rojo C, Cruz-Escurra NDL, Benítes-Zapata VA. Humoral Response after a Fourth Dose with mRNA-1273 in Healthcare Workers with and without a History of SARS-CoV-2 Infection and Previously Vaccinated with Two Doses of BBIBP-CorV Plus BNT162b2 Vaccine. Vaccines (Basel) 2023; 11:vaccines11050894. [PMID: 37242998 DOI: 10.3390/vaccines11050894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 05/28/2023] Open
Abstract
There is limited information on the kinetics of the humoral response elicited by a fourth dose with a heterologous mRNA1273 booster in patients who previously received a third dose with BNT162b2 and two doses of BBIBP-CorV as the primary regimen. We conducted a prospective cohort study to assess the humoral response using Elecsys® anti-SARS-CoV-2 S (anti-S-RBD) of 452 healthcare workers (HCWs) in a private laboratory in Lima, Peru at 21, 120, 210, and 300 days after a third dose with a BNT162b2 heterologous booster in HCW previously immunized with two doses of BBIBP-CorV, depending on whether or not they received a fourth dose with the mRNA1273 heterologous vaccine and on the history of previous SARS infection -CoV-2. Of the 452 HCWs, 204 (45.13%) were previously infected (PI) with SARS-CoV-2, and 215 (47.57%) received a fourth dose with a heterologous mRNA-1273 booster. A total of 100% of HCWs presented positive anti-S-RBD 300 days after the third dose. In HCWs receiving a fourth dose, GMTs 2.3 and 1.6 times higher than controls were observed 30 and 120 days after the fourth dose. No statistically significant differences in anti-S-RBD titers were observed in those HCWs PI and NPI during the follow-up period. We observed that HCWs who received a fourth dose with the mRNA1273 and those previously infected after the third dose with BNT162b2 (during the Omicron wave) presented higher anti-S-RBD titers (5734 and 3428 U/mL, respectively). Further studies are required to determine whether patients infected after the third dose need a fourth dose.
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Affiliation(s)
| | - Miguel Hueda-Zavaleta
- Hospital III Daniel Alcides Carrión, Essalud, Calana Road, Km 6.5, Calana, Tacna 23000, Peru
- Facultad de Ciencias de la Salud, Universidad Privada de Tacna, Bolognesi Avenue Number 1177, Tacna 23003, Peru
| | | | - Cecilia Muro-Rojo
- Roe Clinical Laboratory, Dos de Mayo Avenue, 1741, San Isidro, Lima 15076, Peru
| | | | - Vicente A Benítes-Zapata
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, La Fontana Avenue 550, La Molina, Lima 15024, Peru
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42
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Kavazović I, Dimitropoulos C, Gašparini D, Rončević Filipović M, Barković I, Koster J, Lemmermann NA, Babić M, Cekinović Grbeša Đ, Wensveen FM. Vaccination provides superior in vivo recall capacity of SARS-CoV-2-specific memory CD8 T cells. Cell Rep 2023; 42:112395. [PMID: 37099427 PMCID: PMC10070771 DOI: 10.1016/j.celrep.2023.112395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/07/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Memory CD8 T cells play an important role in the protection against breakthrough infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whether the route of antigen exposure impacts these cells at a functional level is incompletely characterized. Here, we compare the memory CD8 T cell response against a common SARS-CoV-2 epitope after vaccination, infection, or both. CD8 T cells demonstrate comparable functional capacity when restimulated directly ex vivo, independent of the antigenic history. However, analysis of T cell receptor usage shows that vaccination results in a narrower scope than infection alone or in combination with vaccination. Importantly, in an in vivo recall model, memory CD8 T cells from infected individuals show equal proliferation but secrete less tumor necrosis factor (TNF) compared with those from vaccinated people. This difference is negated when infected individuals have also been vaccinated. Our findings shed more light on the differences in susceptibility to re-infection after different routes of SARS-CoV-2 antigen exposure.
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Affiliation(s)
- Inga Kavazović
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | | | - Dora Gašparini
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | | | - Igor Barković
- Department of Internal Medicine, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Jan Koster
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, 1105AZ Amsterdam, the Netherlands
| | - Niels A Lemmermann
- Institute for Virology and Research Center for Immunotherapy (FZI) at the University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Marina Babić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; Innate Immunity, German Rheumatism Research Centre-a Leibniz Institute, 10117 Berlin, Germany
| | | | - Felix M Wensveen
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia.
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Pieren DKJ, Kuguel SG, Rosado J, Robles AG, Rey-Cano J, Mancebo C, Esperalba J, Falcó V, Buzón MJ, Genescà M. Limited induction of polyfunctional lung-resident memory T cells against SARS-CoV-2 by mRNA vaccination compared to infection. Nat Commun 2023; 14:1887. [PMID: 37019909 PMCID: PMC10074357 DOI: 10.1038/s41467-023-37559-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Resident memory T cells (TRM) present at the respiratory tract may be essential to enhance early SARS-CoV-2 viral clearance, thus limiting viral infection and disease. While long-term antigen-specific TRM are detectable beyond 11 months in the lung of convalescent COVID-19 patients, it is unknown if mRNA vaccination encoding for the SARS-CoV-2 S-protein can induce this frontline protection. Here we show that the frequency of CD4+ T cells secreting IFNγ in response to S-peptides is variable but overall similar in the lung of mRNA-vaccinated patients compared to convalescent-infected patients. However, in vaccinated patients, lung responses present less frequently a TRM phenotype compared to convalescent infected individuals and polyfunctional CD107a+ IFNγ+ TRM are virtually absent in vaccinated patients. These data indicate that mRNA vaccination induces specific T cell responses to SARS-CoV-2 in the lung parenchyma, although to a limited extend. It remains to be determined whether these vaccine-induced responses contribute to overall COVID-19 control.
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Affiliation(s)
- Daan K J Pieren
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Sebastián G Kuguel
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Joel Rosado
- Thoracic Surgery and Lung Transplantation Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Alba G Robles
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Joan Rey-Cano
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Cristina Mancebo
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Vicenç Falcó
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - María J Buzón
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Meritxell Genescà
- Infectious Diseases Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.
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Zornikova KV, Sheetikov SA, Rusinov AY, Iskhakov RN, Bogolyubova AV. Architecture of the SARS-CoV-2-specific T cell repertoire. Front Immunol 2023; 14:1070077. [PMID: 37020560 PMCID: PMC10067759 DOI: 10.3389/fimmu.2023.1070077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The T cell response plays an indispensable role in the early control and successful clearance of SARS-CoV-2 infection. However, several important questions remain about the role of cellular immunity in COVID-19, including the shape and composition of disease-specific T cell repertoires across convalescent patients and vaccinated individuals, and how pre-existing T cell responses to other pathogens—in particular, common cold coronaviruses—impact susceptibility to SARS-CoV-2 infection and the subsequent course of disease. This review focuses on how the repertoire of T cell receptors (TCR) is shaped by natural infection and vaccination over time. We also summarize current knowledge regarding cross-reactive T cell responses and their protective role, and examine the implications of TCR repertoire diversity and cross-reactivity with regard to the design of vaccines that confer broader protection against SARS-CoV-2 variants.
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Affiliation(s)
- Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Yu Rusinov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam N. Iskhakov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Apollinariya V. Bogolyubova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- *Correspondence: Apollinariya V. Bogolyubova,
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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46
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Koutsakos M, Reynaldi A, Lee WS, Nguyen J, Amarasena T, Taiaroa G, Kinsella P, Liew KC, Tran T, Kent HE, Tan HX, Rowntree LC, Nguyen THO, Thomas PG, Kedzierska K, Petersen J, Rossjohn J, Williamson DA, Khoury D, Davenport MP, Kent SJ, Wheatley AK, Juno JA. SARS-CoV-2 breakthrough infection induces rapid memory and de novo T cell responses. Immunity 2023; 56:879-892.e4. [PMID: 36958334 PMCID: PMC9970913 DOI: 10.1016/j.immuni.2023.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/26/2023] [Accepted: 02/24/2023] [Indexed: 03/24/2023]
Abstract
Although the protective role of neutralizing antibodies against COVID-19 is well established, questions remain about the relative importance of cellular immunity. Using 6 pMHC multimers in a cohort with early and frequent sampling, we define the phenotype and kinetics of recalled and primary T cell responses following Delta or Omicron breakthrough infection in previously vaccinated individuals. Recall of spike-specific CD4+ T cells was rapid, with cellular proliferation and extensive activation evident as early as 1 day post symptom onset. Similarly, spike-specific CD8+ T cells were rapidly activated but showed variable degrees of expansion. The frequency of activated SARS-CoV-2-specific CD8+ T cells at baseline and peak inversely correlated with peak SARS-CoV-2 RNA levels in nasal swabs and accelerated viral clearance. Our study demonstrates that a rapid and extensive recall of memory T cell populations occurs early after breakthrough infection and suggests that CD8+ T cells contribute to the control of viral replication in breakthrough SARS-CoV-2 infections.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Julie Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen E Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Jan Petersen
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - David Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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Krifors A, Freyhult E, Rashid Teljebäck M, Wallin RPA, Winqvist O, Månsson E. Long-lasting T-cell response to SARS-CoV-2 antigens after vaccination-a prospective cohort study of HCWs working with COVID-19 patients. Infect Dis (Lond) 2023; 55:142-148. [PMID: 36369711 DOI: 10.1080/23744235.2022.2142662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Vaccination against SARS-CoV-2 reduces the risk of hospitalisation and death, but vaccine-induced IgG antibodies against the spike protein (IgG S) decline over time. Less is known about the nature of the vaccine-induced T-cell response to SARS-CoV-2 antigens. METHODS IgG antibodies against nucleocapsid protein (IgG N), IgG S, and T-cell response towards SARS-CoV-2 antigens were determined in samples taken between November 2020 and November 2021 from a cohort of healthcare workers at an Infectious Diseases Department. RT-PCR screening for SARS-CoV-2 was encouraged once every four weeks in addition to testing when symptomatic or identified through contact tracing. Vaccination data were collected at the end of the study. RESULTS At inclusion, T-cell response to SARS-CoV-2 antigens was found in 10/15 (66.7%) of participants with a previous/current COVID-19 infection and in 9/54 (16.7%) of participants with no prior/current history of COVID-19 infection. All participants with complete follow-up (n = 59) received two doses of a SARS-CoV-2 vaccine during the study. All participants demonstrated detectable IgG (S) antibodies at the end of the study, in median 278 days (IQR 112) after the second vaccine dose. All but four participants displayed T-cell responses towards SARS-CoV-2 antigens. IgG S antibody levels correlated with time since the second vaccine dose. In addition, previous COVID-19 infection and the strength of the S1 T-cell response correlated with IgG S antibody levels. However, no correlation was demonstrated between the strength of the T-cell response and time since the second vaccine dose. CONCLUSION COVID-19 vaccination induces robust T-cell responses that remain for at least nine months.
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Affiliation(s)
- Anders Krifors
- Department of Infectious Diseases, Västmanlands Hospital, Västerås, Sweden.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Centre of Clinical Research, Region Västmanland-Uppsala University, Västerås, Sweden
| | - Elisabeth Freyhult
- Department of Laboratory Medicine, Västmanlands Hospital, Västerås, Sweden
| | | | | | | | - Emeli Månsson
- Department of Infectious Diseases, Västmanlands Hospital, Västerås, Sweden.,Centre of Clinical Research, Region Västmanland-Uppsala University, Västerås, Sweden.,Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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48
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Meyer S, Blaas I, Bollineni RC, Delic-Sarac M, Tran TT, Knetter C, Dai KZ, Madssen TS, Vaage JT, Gustavsen A, Yang W, Nissen-Meyer LSH, Douvlataniotis K, Laos M, Nielsen MM, Thiede B, Søraas A, Lund-Johansen F, Rustad EH, Olweus J. Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants. Cell Rep 2023; 42:111995. [PMID: 36656713 PMCID: PMC9826989 DOI: 10.1016/j.celrep.2023.111995] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) is driven by mutations that mediate escape from neutralizing antibodies. There is also evidence that mutations can cause loss of T cell epitopes. However, studies on viral escape from T cell immunity have been hampered by uncertain estimates of epitope prevalence. Here, we map and quantify CD8 T cell responses to SARS-CoV-2-specific minimal epitopes in blood drawn from April to June 2020 from 83 COVID-19 convalescents. Among 37 HLA ligands eluted from five prevalent alleles and an additional 86 predicted binders, we identify 29 epitopes with an immunoprevalence ranging from 3% to 100% among individuals expressing the relevant HLA allele. Mutations in VOC are reported in 10.3% of the epitopes, while 20.6% of the non-immunogenic peptides are mutated in VOC. The nine most prevalent epitopes are conserved in VOC. Thus, comprehensive mapping of epitope prevalence does not provide evidence that mutations in VOC are driven by escape of T cell immunity.
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Affiliation(s)
- Saskia Meyer
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Isaac Blaas
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Trung T. Tran
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Cathrine Knetter
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ke-Zheng Dai
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | | | - John T. Vaage
- Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Alice Gustavsen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Weiwen Yang
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | | | - Karolos Douvlataniotis
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway,ImmunoLingo Convergence Center, University of Oslo, 0372 Oslo, Norway
| | - Even H. Rustad
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
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49
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Pushpakumara PD, Jeewandara C, Bary F, Madushanka D, Perera L, Aberathna IS, Nimasha T, Jayamali J, Ranasinghe T, Kuruppu H, Danasekara S, Wijewickrama A, Ogg GS, Malavige GN. Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.05.23284247. [PMID: 36656781 PMCID: PMC9844014 DOI: 10.1101/2023.01.05.23284247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background As there are limited data on B cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Methods Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n=30), WT infected (n=30), delta infected (n=30), omicron infected+vaccinated (n=20) and Sinopharm (BBIBP-CorV) vaccinees (n=30). We then investigated the sensitivity and specificity of these immunodominant regions and analysed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses and bat Sarbecoviruses. We then investigated the kinetics of responses to these regions in those with varying severity of acute COVID-19. Results We identified four immunodominant regions aa 29-52, aa 155-178, aa 274 to 297 and aa 365 to 388, were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, with WT infected individuals predominantly recognizing aa155 to 178 regions, delta infected individuals and vaccinated+omicron infected individuals predominantly recognizing regions aa 29 to 52 and aa 274 to 294 regions. Sinopharm vaccinees recognized all four regions, with the magnitude of responses significantly lower than other groups. >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. Conclusions N-protein specific responses appear to be detectable in over 90% of those who were naturally infected or vaccinated with a whole virus inactivated vaccine, with responses mainly directed against four regions of the protein, which were highly conserved. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.
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Affiliation(s)
- Pradeep D Pushpakumara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Farha Bary
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshan Madushanka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Lahiru Perera
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Inoka Sepali Aberathna
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thashmi Nimasha
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jeewantha Jayamali
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thushali Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Heshan Kuruppu
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Saubhagya Danasekara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Graham S Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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50
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Soni M, Migliori E, Fu J, Assal A, Chan HT, Pan J, Khatiwada P, Ciubotariu R, May MS, Pereira M, De Giorgi V, Sykes M, Mapara MY, Muranski P. The prospect of universal coronavirus immunity: a characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.519511. [PMID: 36711835 PMCID: PMC9881858 DOI: 10.1101/2023.01.03.519511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
T cell immunity plays a central role in clinical outcomes of Coronavirus Infectious Disease 2019 (COVID-19). Therefore, T cell-focused vaccination or cellular immunotherapy might provide enhanced protection for immunocompromised patients. Pre-existing T cell memory recognizing SARS-CoV2 antigens antedating COVID-19 infection or vaccination, may have developed as an imprint of prior infections with endemic non-SARS human coronaviruses (hCoVs) OC43, HKU1, 229E, NL63, pathogens of "common cold". In turn, SARS-CoV2-primed T cells may recognize emerging variants or other hCoV viruses and modulate the course of subsequent hCoV infections. Cross-immunity between hCoVs and SARS-CoV2 has not been well characterized. Here, we systematically investigated T cell responses against the immunodominant SARS-CoV2 spike, nucleocapsid and membrane proteins and corresponding antigens from α- and β-hCoVs among vaccinated, convalescent, and unexposed subjects. Broad T cell immunity against all tested SARS-CoV2 antigens emerged in COVID-19 survivors. In convalescent and in vaccinated individuals, SARS-CoV2 spike-specific T cells reliably recognized most SARS-CoV2 variants, however cross-reactivity against the omicron variant was reduced by approximately 50%. Responses against spike, nucleocapsid and membrane antigens from endemic hCoVs were more extensive in COVID-19 survivors than in unexposed subjects and displayed cross-reactivity between α- and β-hCoVs. In some, non-SARS hCoVspecific T cells demonstrated a prominent non-reciprocal cross-reactivity with SARS-CoV2 antigens, whereas a distinct anti-SARS-CoV2 immunological repertoire emerged post-COVID-19, with relatively limited cross-recognition of non-SARS hCoVs. Based on this cross-reactivity pattern, we established a strategy for in-vitro expansion of universal anti-hCoV T cells for adoptive immunotherapy. Overall, these results have implications for the future design of universal vaccines and cell-based immune therapies against SARS- and non-SARS-CoVs.
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Affiliation(s)
- Mithil Soni
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
| | - Edoardo Migliori
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
| | - Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
| | - Amer Assal
- Department of Medicine, Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, New York, USA
- Columbia University Medical Center/Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Hei Ton Chan
- Columbia University Medical Center/Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Jian Pan
- Columbia University Medical Center/Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Prabesh Khatiwada
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
| | - Rodica Ciubotariu
- Columbia University Medical Center/Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Michael S May
- Columbia University Medical Center/Herbert Irving Comprehensive Cancer Center, New York, New York, USA
| | - Marcus Pereira
- Department of Medicine, Division of Infectious Disease, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
- Department of Microbiology and Immunology and Department of Surgery, Columbia University, New York, NY, USA
| | - Markus Y Mapara
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
| | - Pawel Muranski
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, New York, United States
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