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Westphal T, Mader M, Karsten H, Cords L, Knapp M, Schulte S, Hermanussen L, Peine S, Ditt V, Grifoni A, Addo MM, Huber S, Sette A, Lütgehetmann M, Pischke S, Kwok WW, Sidney J, Schulze zur Wiesch J. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4 + T-cell response with pre-primed responses directed against common cold coronaviruses. Front Immunol 2023; 14:1182504. [PMID: 37215095 PMCID: PMC10196118 DOI: 10.3389/fimmu.2023.1182504] [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: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction The nonstructural protein 12 (NSP12) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has a high sequence identity with common cold coronaviruses (CCC). Methods Here, we comprehensively assessed the breadth and specificity of the NSP12-specific T-cell response after in vitro T-cell expansion with 185 overlapping 15-mer peptides covering the entire SARS-CoV-2 NSP12 at single-peptide resolution in a cohort of 27 coronavirus disease 2019 (COVID-19) patients. Samples of nine uninfected seronegative individuals, as well as five pre-pandemic controls, were also examined to assess potential cross-reactivity with CCCs. Results Surprisingly, there was a comparable breadth of individual NSP12 peptide-specific CD4+ T-cell responses between COVID-19 patients (mean: 12.82 responses; range: 0-25) and seronegative controls including pre-pandemic samples (mean: 12.71 responses; range: 0-21). However, the NSP12-specific T-cell responses detected in acute COVID-19 patients were on average of a higher magnitude. The most frequently detected CD4+ T-cell peptide specificities in COVID-19 patients were aa236-250 (37%) and aa246-260 (44%), whereas the peptide specificities aa686-700 (50%) and aa741-755 (36%), were the most frequently detected in seronegative controls. In CCC-specific peptide-expanded T-cell cultures of seronegative individuals, the corresponding SARS-CoV-2 NSP12 peptide specificities also elicited responses in vitro. However, the NSP12 peptide-specific CD4+ T-cell response repertoire only partially overlapped in patients analyzed longitudinally before and after a SARS-CoV-2 infection. Discussion The results of the current study indicate the presence of pre-primed, cross-reactive CCC-specific T-cell responses targeting conserved regions of SARS-CoV-2, but they also underline the complexity of the analysis and the limited understanding of the role of the SARS-CoV-2 specific T-cell response and cross-reactivity with the CCCs.
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Affiliation(s)
- Tim Westphal
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Maria Mader
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marc Lütgehetmann
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Pischke
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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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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Wang L, Peng HY, Pham A, Villazana E, Ballard DJ, Das JK, Kumar A, Xiong X, Song J. T Cell Response to SARS-CoV-2 Coinfection and Comorbidities. Pathogens 2023; 12:321. [PMID: 36839596 PMCID: PMC9965203 DOI: 10.3390/pathogens12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
For the past three years, COVID-19 has become an increasing global health issue. Adaptive immune cells, especially T cells, have been extensively investigated in regard to SARS-CoV-2 infection. However, human health and T cell responses are also impacted by many other pathogens and chronic diseases. We have summarized T cell performance during SARS-CoV-2 coinfection with other viruses, bacteria, and parasites. Furthermore, we distinguished if those altered T cell statuses under coinfection would affect their clinical outcomes, such as symptom severity and hospitalization demand. T cell alteration in diabetes, asthma, and hypertension patients with SARS-CoV-2 infection was also investigated in our study. We have summarized whether changes in T cell response influence the clinical outcome during comorbidities.
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Affiliation(s)
- Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Aspen Pham
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Eber Villazana
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Darby J. Ballard
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
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4
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Special Issue "SARS-CoV-2 Innate and Adaptive Immune Responses". Viruses 2022; 14:v14112363. [PMID: 36366460 PMCID: PMC9695004 DOI: 10.3390/v14112363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 01/31/2023] Open
Abstract
Since the end of 2019, humanity has been facing the emergence of a new large positive-sense, single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes a respiratory disease with substantial morbidity and mortality called coronavirus disease 19 (COVID-19) [...]
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Karsten H, Cords L, Westphal T, Knapp M, Brehm TT, Hermanussen L, Omansen TF, Schmiedel S, Woost R, Ditt V, Peine S, Lütgehetmann M, Huber S, Ackermann C, Wittner M, Addo MM, Sette A, Sidney J, Schulze Zur Wiesch J. High-resolution analysis of individual spike peptide-specific CD4 + T-cell responses in vaccine recipients and COVID-19 patients. Clin Transl Immunology 2022; 11:e1410. [PMID: 35957961 PMCID: PMC9363231 DOI: 10.1002/cti2.1410] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives Potential differences in the breadth, distribution and magnitude of CD4+ T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein between vaccinees, COVID‐19 patients and subjects who experienced both ways of immunisation have not been comprehensively compared on a peptide level. Methods Following virus‐specific in vitro cultivation, we determined the T‐cell responses directed against 253 individual overlapping 15‐mer peptides covering the entire SARS‐CoV‐2 spike glycoprotein using IFN‐γ ELISpot and intracellular cytokine staining. In vitro HLA binding was determined for selected peptides. Results We mapped 955 single peptide‐specific CD4+ T‐cell responses in a cohort of COVID‐19 patients (n = 8), uninfected vaccinees (n = 16) and individuals who experienced both infection and vaccination (n = 11). Patients and vaccinees (two‐time and three‐time vaccinees alike) had a comparable number of CD4+ T‐cell responses (median 26 vs. 29, P = 0.7289). Most of these specificities were conserved in B.1.1.529 and the BA.4 and BA.5 sublineages. The highest magnitude of these in vitro IFN‐γ CD4+ T‐cell responses was observed in COVID‐19 patients (median 0.35%), and three‐time vaccinees showed a higher magnitude than two‐time vaccinees (median 0.091% vs. 0.175%, P < 0.0001). Twelve peptide specificities were each detected in at least 40% of subjects. In vitro HLA binding showed promiscuous presentation by DRB1 molecules for several peptides. Conclusion Both SARS‐CoV‐2 infection and vaccination prime broadly directed T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein. This comprehensive high‐resolution analysis of spike peptide specificities will be a useful resource for further investigation of spike‐specific T‐cell responses.
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Affiliation(s)
- Hendrik Karsten
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Leon Cords
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Tim Westphal
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Maximilian Knapp
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Thomas Theo Brehm
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Till Frederik Omansen
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,Department of Tropical Medicine Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Stefan Schmiedel
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Robin Woost
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Sven Peine
- Institute of Transfusion Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Marc Lütgehetmann
- German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany.,Institute of Medical Microbiology, Virology and Hygiene University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Samuel Huber
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Christin Ackermann
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Melanie Wittner
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Marylyn Martina Addo
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany.,Department of Tropical Medicine Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research La Jolla Institute for Immunology (LJI) La Jolla CA USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research La Jolla Institute for Immunology (LJI) La Jolla CA USA
| | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
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