51
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Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563621. [PMID: 37961343 PMCID: PMC10634759 DOI: 10.1101/2023.10.23.563621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.
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Affiliation(s)
- David J. Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Ella Borberg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Zoe Swank
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - David Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
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52
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Goyal A, Bauer J, Hey J, Papageorgiou DN, Stepanova E, Daskalakis M, Scheid J, Dubbelaar M, Klimovich B, Schwarz D, Märklin M, Roerden M, Lin YY, Ma T, Mücke O, Rammensee HG, Lübbert M, Loayza-Puch F, Krijgsveld J, Walz JS, Plass C. DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts. Nat Commun 2023; 14:6731. [PMID: 37872136 PMCID: PMC10593957 DOI: 10.1038/s41467-023-42417-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.
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Affiliation(s)
- Ashish Goyal
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Joschka Hey
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Ekaterina Stepanova
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Daskalakis
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern, University Hospital, University of Bern, Bern, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Marissa Dubbelaar
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Boris Klimovich
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Dominic Schwarz
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yu-Yu Lin
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Ma
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Mücke
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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53
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Seller A, Hackenbruch C, Walz JS, Nelde A, Heitmann JS. Long-Term Follow-Up of COVID-19 Convalescents-Immune Response Associated with Reinfection Rate and Symptoms. Viruses 2023; 15:2100. [PMID: 37896879 PMCID: PMC10611319 DOI: 10.3390/v15102100] [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: 09/08/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 has spread worldwide, causing millions of deaths and leaving a significant proportion of people with long-term sequelae of COVID-19 ("post-COVID syndrome"). Whereas the precise mechanism of post-COVID syndrome is still unknown, the immune response after the first infection may play a role. Here, we performed a long-term follow-up analysis of 110 COVID-19 convalescents, analyzing the first SARS-CoV-2-directed immune response, vaccination status, long-term symptoms (approximately 2.5 years after first infection), and reinfections. A total of 96% of convalescents were vaccinated at least once against SARS-CoV-2 after their first infection. A reinfection rate of 47% was observed, and lower levels of anti-spike IgG antibodies after the first infection were shown to associate with reinfection. While T-cell responses could not be clearly associated with persistent postinfectious symptoms, convalescents with long-term symptoms showed elevated SARS-CoV-2-specific antibody levels at the first infection. Evaluating the immune response after the first infection might be a useful tool for identifying individuals with increased risk for re-infections and long-term symptoms.
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Affiliation(s)
- Anna Seller
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Obstetrics and Gynecology, University Hospital Tuebingen, Calwerstraße 7, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Christopher Hackenbruch
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
| | - Annika Nelde
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
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54
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Kam NW, Lau CY, Che CM, Lee VHF. Nasopharynx Battlefield: Cellular Immune Responses Mediated by Midkine in Nasopharyngeal Carcinoma and COVID-19. Cancers (Basel) 2023; 15:4850. [PMID: 37835544 PMCID: PMC10571800 DOI: 10.3390/cancers15194850] [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: 06/19/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Clinical evidence suggests that the severe respiratory illness coronavirus disease 2019 (COVID-19) is often associated with a cytokine storm that results in dysregulated immune responses. Prolonged COVID-19 positivity is thought to disproportionately affect cancer patients. With COVID-19 disrupting the delivery of cancer care, it is crucial to gain momentum and awareness of the mechanistic intersection between these two diseases. This review discusses the role of the cytokine midkine (MK) as an immunomodulator in patients with COVID-19 and nasopharyngeal carcinoma (NPC), both of which affect the nasal cavity. We conducted a review and analysis of immunocellular similarities and differences based on clinical studies, research articles, and published transcriptomic datasets. We specifically focused on ligand-receptor pairs that could be used to infer intercellular communication, as well as the current medications used for each disease, including NPC patients who have contracted COVID-19. Based on our findings, we recommend close monitoring of the MK axis to maintain the desirable effects of therapeutic regimens in fighting both NPC and COVID-19 infections.
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Affiliation(s)
- Ngar-Woon Kam
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
| | - Cho-Yiu Lau
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong 999077, China
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
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55
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Yeung J, Wang T, Shi PY. Improvement of mucosal immunity by a live-attenuated SARS-CoV-2 nasal vaccine. Curr Opin Virol 2023; 62:101347. [PMID: 37604085 DOI: 10.1016/j.coviro.2023.101347] [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: 01/25/2023] [Accepted: 07/18/2023] [Indexed: 08/23/2023]
Abstract
The effectiveness of early COVID-19 vaccines in reducing the severity of the disease has led to a focus on developing next-generation vaccines that can prevent infection and transmission of the virus. One promising approach involves the induction of mucosal immunity through nasal administration and a variety of mucosal vaccine candidates using different platforms are currently in development. Live-attenuated viruses, less pathogenic versions of SARS-CoV-2, have promising features as a mucosal vaccine platform and have the potential to induce hybrid immunity in individuals who have already received mRNA vaccines. This review discusses the potential benefits and considerations for the use of live-attenuated SARS-CoV-2 intranasal vaccines and highlights the authors' work in developing such a vaccine platform.
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Affiliation(s)
- Jason Yeung
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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56
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Li C, Ma L, Zou D, Zhang R, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y, Song S. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1066-1079. [PMID: 37898309 PMCID: PMC10928372 DOI: 10.1016/j.gpb.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.
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Affiliation(s)
- Cuiping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lun Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
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57
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Goswami A, Kumar M, Ullah S, Gore MM. De novo design of anti-variant COVID-19 vaccine. Biol Methods Protoc 2023; 8:bpad021. [PMID: 37854896 PMCID: PMC10580973 DOI: 10.1093/biomethods/bpad021] [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: 07/28/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Recent studies highlight the effectiveness of hybrid Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) vaccines combining wild-type nucleocapsid and Spike proteins. We have further enhanced this strategy by incorporating delta and omicron variants' spike protein mutations. Both delta and omicron mark the shifts in viral transmissibility and severity in unvaccinated and vaccinated patients. So their mutations are highly crucial for future viral variants also. Omicron is particularly adept at immune evasion by mutating spike epitopes. The rapid adaptations of Omicron and sub-variants to spike-based vaccines and simultaneous transmissibility underline the urgency for new vaccines in the continuous battle against SARS-CoV-2. Therefore, we have added three persistent T-cell-stimulating nucleocapsid peptides similar to homologous sequences from seasonal Human Coronaviruses (HuCoV) and an envelope peptide that elicits a strong T-cell immune response. These peptides are clustered in the hybrid spike's cytoplasmic region with non-immunogenic linkers, enabling systematic arrangement. AlphaFold (Artificial intelligence-based model building) analysis suggests omitting the transmembrane domain enhances these cytoplasmic epitopes' folding efficiency which can ensure persistent immunity for CD4+ structural epitopes. Further molecular dynamics simulations validate the compact conformation of the modeled structures and a flexible C-terminus region. Overall, the structures show stability and less conformational fluctuation throughout the simulation. Also, the AlphaFold predicted structural epitopes maintained their folds during simulation to ensure the specificity of CD4+ T-cell response after vaccination. Our proposed approach may provide options for incorporating diverse anti-viral T-cell peptides, similar to HuCoV, into linker regions. This versatility can be promising to address outbreaks and challenges posed by various viruses for effective management in this era of innovative vaccines.
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Affiliation(s)
- Arpita Goswami
- Kshamalab, Leo’s Research Services and Suppliers, Mysuru 570016, India
| | - Madan Kumar
- Department of Chemistry-BMC Biochemistry, University of Uppsala, Uppsala 75237, Sweden
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad 45320, Pakistan
| | - Milind M Gore
- 5/1B, Krutika Co-Op Housing Society, Kothrud, Pune 411039, India
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58
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Mahalingam SS, Jayaraman S, Arunkumar A, Dudley HM, Anthony DD, Shive CL, Jacobson JM, Pandiyan P. Distinct SARS-CoV-2 specific NLRP3 and IL-1β responses in T cells of aging patients during acute COVID-19 infection. Front Immunol 2023; 14:1231087. [PMID: 37799713 PMCID: PMC10548880 DOI: 10.3389/fimmu.2023.1231087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19) that presents with varied clinical manifestations ranging from asymptomatic or mild infections and pneumonia to severe cases associated with cytokine storm, acute respiratory distress syndrome (ARDS), and even death. The underlying mechanisms contributing to these differences are unclear, although exacerbated inflammatory sequelae resulting from infection have been implicated. While advanced aging is a known risk factor, the precise immune parameters that determine the outcome of SARS-CoV-2 infection in elderly individuals are not understood. Here, we found aging-associated (age ≥61) intrinsic changes in T cell responses when compared to those from individuals aged ≤ 60, even among COVID-positive patients with mild symptoms. Specifically, when stimulated with SARS-CoV-2 peptides in vitro, peripheral blood mononuclear cell (PBMC) CD4+ and CD8+ T cells from individuals aged ≥61 showed a diminished capacity to produce IFN-γ and IL-1β. Although they did not have severe disease, aged individuals also showed a higher frequency of PD-1+ cells and significantly diminished IFN-γ/PD-1 ratios among T lymphocytes upon SARS-CoV-2 peptide stimulation. Impaired T cell IL-1β expression coincided with reduced NLRP3 levels in T lymphocytes. However, the expression of these molecules was not affected in the monocytes of individuals aged ≥61. Together, these data reveal SARS-CoV-2-specific CD4+ and CD8+ T-cell intrinsic cytokine alterations in the individuals older than 61 and may provide new insights into dysregulated COVID-directed immune responses in the elderly.
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Affiliation(s)
- Shanmuga Sundaram Mahalingam
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Sangeetha Jayaraman
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Adhvika Arunkumar
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Holly M. Dudley
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Donald D. Anthony
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, University Hospitals, Case Western Reserve University, Cleveland, OH, United States
| | - Carey L. Shive
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Jeffrey M. Jacobson
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, University Hospitals, Case Western Reserve University, Cleveland, OH, United States
| | - Pushpa Pandiyan
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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59
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Fathollahi M, Motamedi H, Hossainpour H, Abiri R, Shahlaei M, Moradi S, Dashtbin S, Moradi J, Alvandi A. Designing a novel multi-epitopes pan-vaccine against SARS-CoV-2 and seasonal influenza: in silico and immunoinformatics approach. J Biomol Struct Dyn 2023:1-24. [PMID: 37723861 DOI: 10.1080/07391102.2023.2258420] [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: 06/02/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
Abstract
The merger of COVID-19 and seasonal influenza infections is considered a potentially serious threat to public health. These two viral agents can cause extensive and severe lower and upper respiratory tract infections with lung damage with host factors. Today, the development of vaccination has been shown to reduce the risk of hospitalization and mortality from the COVID-19 virus and influenza epidemics. Therefore, this study contributes to an immunoinformatics approach to producing a vaccine that can elicit strong and specific immune responses against COVID-19 and influenza A and B viruses. The NCBI, GISAID, and Uniprot databases were used to retrieve sequences. Linear B cell, Cytotoxic T lymphocyte, and Helper T lymphocyte epitopes were predicted using the online servers. Population coverage of MHC I epitopes worldwide for SARS-CoV-2, Influenza virus H3N2, H3N2, and Yamagata/Victoria were 99.93%, 68.67%, 68.38%, and 85.45%, respectively. Candidate epitopes were linked by GGGGS, GPGPG, and KK linkers. Different epitopes were permutated several times to form different peptides and then screened for antigenicity, allergenicity, and toxicity. The vaccine construct was analyzed for physicochemical properties, conformational B-cell epitopes, interaction with Toll-like receptors, and IFN-gamma-induced. Immune stimulation response of final construct was evaluated using C-IMMSIM. Eventually, the final construct sequence was codon-optimized for Escherichia coli K12 and Homo sapiens to design a multi-epitope vaccine and mRNA vaccine. In conclusion, due to the variable nature of SARS-CoV-2 and influenza proteins, the design of a multi-epitope vaccine can protect against all their standard variants, but laboratory validation is required.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Matin Fathollahi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid Motamedi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hadi Hossainpour
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shirin Dashtbin
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jale Moradi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
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60
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Yajima Y, Kosaka A, Ohkuri T, Hirohashi Y, Li D, Nagasaki T, Nagato T, Torigoe T, Kobayashi H. SARS-CoV-2 spike protein-derived immunogenic peptides that are promiscuously presented by several HLA-class II molecules and their potential for inducing acquired immunity. Heliyon 2023; 9:e20192. [PMID: 37809871 PMCID: PMC10559948 DOI: 10.1016/j.heliyon.2023.e20192] [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: 12/10/2022] [Revised: 05/26/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic that is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a significant threat to public health. Although vaccines based on the mRNA of the SARS-CoV-2 spike protein have been developed to induce both cellular and humoral immunity against SARS-CoV-2, there have been some concerns raised about their high cost, particularly in developing countries. In the present study, we aim to identify an immunogenic peptide in the SARS-CoV-2 spike protein to activate cellular immunity, particularly CD4+ helper T lymphocytes (Th cells), which are a commander of immune system. SARS-CoV-2 spike protein-derived peptides Spike448-477 and Spike489-513(N501Y)-specific CD4+ Th cell lines were generated by repetitive stimulation of healthy donor-derived CD4+T-cells with each peptide. Their HLA-restrictions were addressed by using blocking antibodies against HLA and HLA-transfected L-cells. The epitopes of Spike448-477-specific CD4+ Th cell lines were defined using a series of 7-14-mer overlapping truncated peptides and alanine-substituted epitope peptides. To address responsiveness of these CD4+ Th cell lines to several SARS-CoV-2 variants, we stimulated the CD4+ Th cell lines with mutated peptides. We addressed whether these identified peptides were useful for monitoring T-cell-based immune responses in vaccinated donors using the IFN-γ ELISpot assay. The Spike448-477 peptide was found to be a promiscuous peptide presented by HLA- DRB1*08:02, DR53, and DPB1*02:02. Although HLA-DPB1*02:02-restricted CD4+ Th cells did not response to some peptides with the L452R and L452Q mutations, the other CD4+ Th cells were not affected by any mutant peptides. We developed two tetramers to detect HLA-DRB1*08:02/Spike449-463- and Spike449-463(L452R/Y453F)-recognizing CD4+ Th cells. Spike489-513(N501Y) peptide was also a promiscuously presented to HLA-DRB1*09:01 and DRB1*15:02. The T-cell responses specific to both peptides Spike448-477 and Spike489-513 were detected in PBMCs after vaccinations. In addition, we observed that the Spike448-477 peptide activated both CD8+ T-cells and CD4+ Th cells in individuals receiving mRNA vaccines. SARS-CoV-2 spike protein-derived peptides, Spike448-477 and Spike489-513, include several epitopes that are presented by multiple HLA-class II alleles to activate CD4+ Th cells, which are considered useful for monitoring the establishment of acquired immunity after vaccination.
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Affiliation(s)
- Yuki Yajima
- Department of Oral and Maxillofacial Surgery, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Akemi Kosaka
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takayuki Ohkuri
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Yoshihiko Hirohashi
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Dongliang Li
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd., Ina, Japan
| | - Takeshi Nagasaki
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd., Ina, Japan
| | - Toshihiro Nagato
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroya Kobayashi
- Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
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61
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Allers K, Moos V, Hofmann J, Witkowski M, Haibel H, Angermair S, Schneider T. Cytolytic CD8 + T cell response to SARS-CoV-2 and non-SARS-CoV-2-related viruses is associated with severe manifestation of COVID-19. Clin Immunol 2023; 254:109712. [PMID: 37506745 DOI: 10.1016/j.clim.2023.109712] [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: 03/23/2023] [Revised: 04/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Little is known about the CD8+ T cell functionality in the coronavirus disease 2019 (COVID-19). Therefore, we examined twenty-five hospitalized COVID-19 patients with moderate (MD) or severe disease (SD) as well as seventeen SARS-CoV-2-unexposed persons regarding the cytolytic and cytokine-producing reactivity of their CD8+ T cells. Reactive CD8+ T cells were detectable in 90% of the unexposed persons, confirming high cross-reactive immune memory in the general population. Compared to unexposed persons and MD patients, SD patients had higher numbers of SARS-CoV-2 reactive CD8+ T cells with cytolytic function that can simultaneously produce inflammatory cytokines. In addition, SD patients showed higher CD8+ T cell reactivity against non-SARS-CoV-2-related viruses, which was mainly mediated by cytolytic response. Sequence alignments showed that cross-reactivities with the Spike protein could contribute to the expansion of such cells. Since insufficiently regulated cytolytic CD8+ T cells can damage peripheral and vascular tissue structures, high levels of both SARS-CoV-2-reactive and heterologously activated cytolytic CD8+ T cells could favor severe disease progression.
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Affiliation(s)
- Kristina Allers
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany.
| | - Verena Moos
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Jörg Hofmann
- Labor Berlin - Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Mario Witkowski
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Microbiology, Infectious Diseases and Immunology, Laboratory of Innate Immunity, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Hildrun Haibel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Stefan Angermair
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Klinik für Anästhesiologie mit Schwerpunkt operative Intensivmedizin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Thomas Schneider
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
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62
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Chen Y, Mason GH, Scourfield DO, Greenshields-Watson A, Haigh TA, Sewell AK, Long HM, Gallimore AM, Rizkallah P, MacLachlan BJ, Godkin A. Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Cell Rep 2023; 42:112827. [PMID: 37471227 PMCID: PMC10840515 DOI: 10.1016/j.celrep.2023.112827] [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: 03/08/2023] [Revised: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.
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Affiliation(s)
- Yuan Chen
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Georgina H Mason
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - D Oliver Scourfield
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Tracey A Haigh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Awen M Gallimore
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Pierre Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Andrew Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Department of Gastroenterology & Hepatology, University Hospital of Wales, Cardiff CF14 4XW, UK.
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63
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Kanis FM, Meier JP, Guldan H, Niller HH, Dahm M, Dansard A, Zander T, Struck F, Soutschek E, Deml L, Möbus S, Barabas S. Performance of T-Track ® SARS-CoV-2, an Innovative Dual Marker RT-qPCR-Based Whole-Blood Assay for the Detection of SARS-CoV-2-Reactive T Cells. Diagnostics (Basel) 2023; 13:2722. [PMID: 37685260 PMCID: PMC10486492 DOI: 10.3390/diagnostics13172722] [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: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
T-cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a central role in the control of the virus. In this study, we evaluated the performance of T-Track® SARS-CoV-2, a novel CE-marked quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay, which relies on the combined evaluation of IFNG and CXCL10 mRNA levels in response to the S1 and NP SARS-CoV-2 antigens, in 335 participants with or without a history of SARS-CoV-2 infection and vaccination, respectively. Of the 62 convalescent donors, 100% responded to S1 and 88.7% to NP antigens. In comparison, of the 68 naïve donors, 4.4% were reactive to S1 and 19.1% to NP. Convalescent donors <50 and ≥50 years of age demonstrated a 100% S1 reactivity and an 89.1% and 87.5% NP reactivity, respectively. T-cell responses by T-Track® SARS-CoV-2 and IgG serology by recomLine SARS-CoV-2 IgG according to the time from the last immunisation (by vaccination or viral infection) were comparable. Both assays showed a persistent cellular and humoral response for at least 36 weeks post immunisation in vaccinated and convalescent donors. Our results demonstrate the very good performance of the T-Track® SARS-CoV-2 molecular assay and suggest that it might be suitable to monitor the SARS-CoV-2-specific T-cell response in COVID-19 vaccinations trials and cross-reactivity studies.
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Affiliation(s)
| | | | | | - Hans-Helmut Niller
- Institute for Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany
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64
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Heitmann JS, Tandler C, Marconato M, Nelde A, Habibzada T, Rittig SM, Tegeler CM, Maringer Y, Jaeger SU, Denk M, Richter M, Oezbek MT, Wiesmüller KH, Bauer J, Rieth J, Wacker M, Schroeder SM, Hoenisch Gravel N, Scheid J, Märklin M, Henrich A, Klimovich B, Clar KL, Lutz M, Holzmayer S, Hörber S, Peter A, Meisner C, Fischer I, Löffler MW, Peuker CA, Habringer S, Goetze TO, Jäger E, Rammensee HG, Salih HR, Walz JS. Phase I/II trial of a peptide-based COVID-19 T-cell activator in patients with B-cell deficiency. Nat Commun 2023; 14:5032. [PMID: 37596280 PMCID: PMC10439231 DOI: 10.1038/s41467-023-40758-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
T-cell immunity is central for control of COVID-19, particularly in patients incapable of mounting antibody responses. CoVac-1 is a peptide-based T-cell activator composed of SARS-CoV-2 epitopes with documented favorable safety profile and efficacy in terms of SARS-CoV-2-specific T-cell response. We here report a Phase I/II open-label trial (NCT04954469) in 54 patients with congenital or acquired B-cell deficiency receiving one subcutaneous CoVac-1 dose. Immunogenicity in terms of CoVac-1-induced T-cell responses and safety are the primary and secondary endpoints, respectively. No serious or grade 4 CoVac-1-related adverse events have been observed. Expected local granuloma formation has been observed in 94% of study subjects, whereas systemic reactogenicity has been mild or absent. SARS-CoV-2-specific T-cell responses have been induced in 86% of patients and are directed to multiple CoVac-1 peptides, not affected by any current Omicron variants and mediated by multifunctional T-helper 1 CD4+ T cells. CoVac-1-induced T-cell responses have exceeded those directed to the spike protein after mRNA-based vaccination of B-cell deficient patients and immunocompetent COVID-19 convalescents with and without seroconversion. Overall, our data show that CoVac-1 induces broad and potent T-cell responses in patients with B-cell/antibody deficiency with a favorable safety profile, which warrants advancement to pivotal Phase III safety and efficacy evaluation. ClinicalTrials.gov identifier NCT04954469.
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Affiliation(s)
- Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Claudia Tandler
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Maddalena Marconato
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Timorshah Habibzada
- Institute of Clinical Cancer Research, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Susanne M Rittig
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Christian M Tegeler
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Simon U Jaeger
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Monika Denk
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Marion Richter
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Melek T Oezbek
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | - Jens Bauer
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Naomi Hoenisch Gravel
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Scheid
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Henrich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Boris Klimovich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Kim L Clar
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Martina Lutz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Samuel Holzmayer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Meisner
- Robert Bosch Hospital, Robert Bosch Society for Medical Research, Stuttgart, Germany
| | - Imma Fischer
- Institute for Clinical Epidemiology and Applied Biometry, University Hospital Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Caroline Anna Peuker
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Stefan Habringer
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Thorsten O Goetze
- Institute of Clinical Cancer Research, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Elke Jäger
- Department for Oncology and Hematology, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Hans-Georg Rammensee
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
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N’Guessan A, Kailasam S, Mostefai F, Poujol R, Grenier JC, Ismailova N, Contini P, De Palma R, Haber C, Stadler V, Bourque G, Hussin JG, Shapiro BJ, Fritz JH, Piccirillo CA. Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis. iScience 2023; 26:107394. [PMID: 37599818 PMCID: PMC10433132 DOI: 10.1016/j.isci.2023.107394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Here, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses. Applying a high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses allowed identification of B cell epitopes and relate them to their evolutionary and structural properties. We identify hotspots of pre-existing immunity and identify cross-reactive epitopes that contribute to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves, and SARS-CoV-2 variants. Lastly, we show that mutations in spike and nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.
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Affiliation(s)
- Arnaud N’Guessan
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Senthilkumar Kailasam
- Canadian Center for Computational Genomics, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Fatima Mostefai
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Raphaël Poujol
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Nailya Ismailova
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Paola Contini
- Department of Internal Medicine, University of Genoa and IRCCS IST-Ospedale San Martino, Genoa, Italy
| | - Raffaele De Palma
- Department of Internal Medicine, University of Genoa and IRCCS IST-Ospedale San Martino, Genoa, Italy
| | | | | | - Guillaume Bourque
- Canadian Center for Computational Genomics, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Julie G. Hussin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
| | - Ciriaco A. Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- McGill University Research Center on Complex Traits (MRCCT), McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program of the Research Institute of McGill Health Center, Montréal, QC, Canada
- Dahdaleh Institute of Genomic Medicine (DIgM), McGill University, Montréal, QC, Canada
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66
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Dang TTT, Anzurez A, Nakayama-Hosoya K, Miki S, Yamashita K, de Souza M, Matano T, Kawana-Tachikawa A. Breadth and Durability of SARS-CoV-2-Specific T Cell Responses following Long-Term Recovery from COVID-19. Microbiol Spectr 2023; 11:e0214323. [PMID: 37428088 PMCID: PMC10433967 DOI: 10.1128/spectrum.02143-23] [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: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
T cell immunity is crucial for long-term immunological memory, but the profile of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific memory T cells in individuals who recovered from COVID-19 (COVID-19-convalescent individuals) is not sufficiently assessed. In this study, the breadth and magnitude of SARS-CoV-2-specific T cell responses were determined in COVID-19-convalescent individuals in Japan. Memory T cells against SARS-CoV-2 were detected in all convalescent individuals, and those with more severe disease exhibited a broader T cell response relative to cases with mild symptoms. Comprehensive screening of T cell responses at the peptide level was conducted for spike (S) and nucleocapsid (N) proteins, and regions frequently targeted by T cells were identified. Multiple regions in S and N proteins were targeted by memory T cells, with median numbers of target regions of 13 and 4, respectively. A maximum of 47 regions were recognized by memory T cells for an individual. These data indicate that SARS-CoV-2-convalescent individuals maintain a substantial breadth of memory T cells for at least several months following infection. Broader SARS-CoV-2-specific CD4+ T cell responses, relative to CD8+ T cell responses, were observed for the S but not the N protein, suggesting that antigen presentation is different between viral proteins. The binding affinity of predicted CD8+ T cell epitopes to HLA class I molecules in these regions was preserved for the Delta variant and at 94 to 96% for SARS-CoV-2 Omicron subvariants, suggesting that the amino acid changes in these variants do not have a major impact on antigen presentation to SARS-CoV-2-specific CD8+ T cells. IMPORTANCE RNA viruses, including SARS-CoV-2, evade host immune responses through mutations. As broader T cell responses against multiple viral proteins could minimize the impact of each single amino acid mutation, the breadth of memory T cells would be one essential parameter for effective protection. In this study, breadth of memory T cells to S and N proteins was assessed in COVID-19-convalescent individuals. While broad T cell responses were induced against both proteins, the ratio of N to S proteins for breadth of T cell responses was significantly higher in milder cases. The breadth of CD4+ and CD8+ T cell responses was also significantly different between S and N proteins, suggesting different contributions of N and S protein-specific T cells for COVID-19 control. Most CD8+ T cell epitopes in the immunodominant regions maintained their HLA binding to SARS-CoV-2 Omicron subvariants. Our study provides insights into understanding the protective efficacy of SARS-CoV-2-specific memory T cells against reinfection.
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Affiliation(s)
- Thi Thu Thao Dang
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Alitzel Anzurez
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | | | - Shoji Miki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Mark de Souza
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Namuniina A, Muyanja ES, Biribawa VM, Okech BA, Ssemaganda A, Price MA, Hills N, Nanteza A, Bagaya BS, Weiskopf D, Riou C, Reynolds SJ, Galiwango RM, Redd AD. Proportion of Ugandans with pre-pandemic SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell responses: A pilot study. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001566. [PMID: 37585383 PMCID: PMC10431628 DOI: 10.1371/journal.pgph.0001566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/12/2023] [Indexed: 08/18/2023]
Abstract
The estimated mortality rate of the SARS-CoV-2 pandemic varied greatly around the world. In particular, multiple countries in East, Central, and West Africa had significantly lower rates of COVID-19 related fatalities than many resource-rich nations with significantly earlier wide-spread access to life-saving vaccines. One possible reason for this lower mortality could be the presence of pre-existing cross-reactive immunological responses in these areas of the world. To explore this hypothesis, an exploratory study of stored peripheral blood mononuclear cells (PBMC) from Ugandans collected from 2015-2017 prior to the COVID-19 pandemic (n = 29) and from hospitalized Ugandan COVID-19 patients (n = 3) were examined using flow-cytometry for the presence of pre-existing SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell populations using four T-cell epitope mega pools. Of pre-pandemic participants, 89.7% (26/29) had either CD4+ or CD8+, or both, SARS-CoV-2 specific T-cell responses. Specifically, CD4+ T-cell reactivity (72.4%) and CD8+ T-cell reactivity (65.5%) were relatively similar, and 13 participants (44.8%) had both types of cross-reactive types of T-cells present. There were no significant differences in response by sex in the population, however this may be in part due to the limited sample size examined. The rates of cross-reactive T-cell populations in this exploratory Ugandan population appears higher than previous estimates from resource-rich countries like the United States (20-50% reactivity). It is unclear what role, if any, this cross-reactivity played in decreasing COVID-19 related mortality in Uganda and other African countries, but does suggest that a better understanding of global pre-existing immunological cross-reactivity could be an informative data of epidemiological intelligence moving forward.
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Affiliation(s)
| | - Enoch S. Muyanja
- PATRU, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | | | | | - Aloysious Ssemaganda
- Rady Faculty of Health Sciences, Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Matt A. Price
- IAVI, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Nancy Hills
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources & Bio-security, Makerere University, Kampala, Uganda
| | - Bernard Ssentalo Bagaya
- Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, Uganda
- Integrated Biorepository of H3-Africa-Uganda (IBRH3AU), COVID-19 Biobank (COV-BANK), College of Health Sciences, Makerere University, Kampala, Uganda
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Catherine Riou
- Department of Pathology, Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Steven J. Reynolds
- Division of Intramural Research, NIAID, NIH, Baltimore Maryland, United States of America
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Andrew D. Redd
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Intramural Research, NIAID, NIH, Baltimore Maryland, United States of America
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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68
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Beitari S, Duque D, Bavananthasivam J, Hewitt M, Sandhu JK, Hadžisejdić I, Tran A. Cross protection to SARS-CoV-2 variants in hamsters with naturally-acquired immunity. Virol J 2023; 20:167. [PMID: 37507719 PMCID: PMC10386765 DOI: 10.1186/s12985-023-02136-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Since SARS-CoV-2 was first reported in late 2019, multiple variations of the original virus have emerged. Each variant harbors accumulations of mutations, particularly within the spike glycoprotein, that are associated with increased viral transmissibility and escape immunity. The different mutations in the spike protein of different variants shape the subsequent antibody and T cell responses, such that exposure to different spike proteins can result in reduced or enhanced responses to heterologous variants further down the line. Globally, people have been exposed and re-exposed to multiple variations of the Ancestral strain, including the five variants of concerns. Studies have shown that the protective immune response of an individual is influenced by which strain or combination of strains they are exposed to. The initial exposure to a specific strain may also shape their subsequent immune patterns and response to later infections with a heterologous virus. Most immunological observations were carried out early during the pandemic when the Ancestral strain was circulating. However, SARS-CoV-2 variants exhibit varying patterns of disease severity, waning immunity, immune evasion and sensitivity to therapeutics. Here we investigated the cross-protection in hamsters previously infected with a variant of concern (VOC) and subsequently re-infected with a heterologous variant. We also determined if cross-protection and immunity were dependent on the specific virus to which the hamster was first exposed. We further profiled the host cytokine response induced by each SARS-CoV-2 variants as well as subsequent to re-infection. A comparative analysis of the three VOCs revealed that Alpha variant was the most pathogenic VOC to emerge. We showed that naturally acquired immunity protected hamsters from subsequent re-infection with heterologous SARS-CoV-2 variant, regardless which variant the animal was first exposed to. Our study supports observations that heterologous infection of different SARS-CoV-2 variants do not exacerbate disease in subsequent re-infections. The continual emergence of new SARS-CoV-2 variants mandates a better understanding of cross-protection and immune imprinting in infected individuals. Such information is essential to guide vaccine strategy and public policy to emerging SARS-CoV-2 VOCs and future novel pandemic coronaviruses.
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Affiliation(s)
- Saina Beitari
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Diana Duque
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jegarubee Bavananthasivam
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Melissa Hewitt
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jagdeep K Sandhu
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Ita Hadžisejdić
- Clinical Department of Pathology and Cytology, University of Rijeka, Rijeka, Croatia
| | - Anh Tran
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada.
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69
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Wu Y, Huang P, Xu M, Zhao Q, Xu Y, Han S, Li H, Wang Y. Immunogenicity and reactogenicity of inactivated SARS-CoV-2 vaccines in healthy adults. Front Immunol 2023; 14:1152899. [PMID: 37559719 PMCID: PMC10407550 DOI: 10.3389/fimmu.2023.1152899] [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: 01/28/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly pathogenic to humans and has caused the ongoing coronavirus disease 2019 (COVID-19) pandemic. Vaccines are one of the efficient ways to prevent the viral infection. After COVID-19 vaccination, the monitoring of the dynamic change in neutralizing antibodies is necessary to determine booster requirements. Methods We estimated the effectiveness of the inactivated vaccines by monitoring dynamic SARS-CoV-2 neutralizing antibodies for over 2 years. Additionally, we also investigated the activation of T lymphocytes (CD3+ T cells) after three doses of the inactivated vaccine. Result The results showed that the rate of reduction of SARS-CoV-2 neutralizing antibody levels gradually showed after each booster dose. The IgG/IgM level at 9 months after the third vaccination were significantly higher than those at 6 months after the second dose (p<0.0001). The expression of CD25+T cell in 18-35 age group was significantly higher than that in the other groups. Nine months after the third dose (the time of last blood sample collection), the expression of CD25+T cell in the 18-35 age group was significantly higher than that at 6 months after the second dose. CD25+T cell in the 18-35 years old group was significantly higher than 6 months after the second vaccination. Conclusion CD25, a late activation marker of lymphocytes and high-activity memory T cell subgroup, exhibited higher levels at the later stages after vaccination. COVID-19 booster vaccination in older adults and regular testing of SARS-CoV-2 neutralizing antibodies are recommended. Booster doses should be administered if the antibody level falls below the 30% inhibition rate.
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Affiliation(s)
- Yufei Wu
- Institute of Medical Sciences, the Second Hospital of Shandong University, Jinan, Shandong, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Ping Huang
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Mingjie Xu
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Qianqian Zhao
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Yihui Xu
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Shuyi Han
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
| | - Huanjie Li
- Institute of Medical Sciences, the Second Hospital of Shandong University, Jinan, Shandong, China
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yunshan Wang
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Research Center of Basic Medicine, Jinan Central Hospital, Shandong University, Jinan, Shandong, China
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70
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Chen M, Venturi V, Munier CML. Dissecting the Protective Effect of CD8 + T Cells in Response to SARS-CoV-2 mRNA Vaccination and the Potential Link with Lymph Node CD8 + T Cells. BIOLOGY 2023; 12:1035. [PMID: 37508464 PMCID: PMC10376827 DOI: 10.3390/biology12071035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
SARS-CoV-2 vaccines have played a crucial role in effectively reducing COVID-19 disease severity, with a new generation of vaccines that use messenger RNA (mRNA) technology being administered globally. Neutralizing antibodies have featured as the heroes of vaccine-induced immunity. However, vaccine-elicited CD8+ T cells may have a significant impact on the early protective effects of the mRNA vaccine, which are evident 12 days after initial vaccination. Vaccine-induced CD8+ T cells have been shown to respond to multiple epitopes of SARS-CoV-2 and exhibit polyfunctionality in the periphery at the early stage, even when neutralizing antibodies are scarce. Furthermore, SARS-CoV-2 mRNA vaccines induce diverse subsets of memory CD8+ T cells that persist for more than six months following vaccination. However, the protective role of CD8+ T cells in response to the SARS-CoV-2 mRNA vaccines remains a topic of debate. In addition, our understanding of CD8+ T cells in response to vaccination in the lymph nodes, where they first encounter antigen, is still limited. This review delves into the current knowledge regarding the protective role of polyfunctional CD8+ T cells in controlling the virus, the response to SARS-CoV-2 mRNA vaccines, and the contribution to supporting B cell activity and promoting immune protection in the lymph nodes.
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Affiliation(s)
- Mengfei Chen
- The Kirby Institute, UNSW, Sydney, NSW 2052, Australia
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71
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Abdelaziz MO, Raftery MJ, Weihs J, Bielawski O, Edel R, Köppke J, Vladimirova D, Adler JM, Firsching T, Voß A, Gruber AD, Hummel LV, Fernandez Munoz I, Müller-Marquardt F, Willimsky G, Elleboudy NS, Trimpert J, Schönrich G. Early protective effect of a ("pan") coronavirus vaccine (PanCoVac) in Roborovski dwarf hamsters after single-low dose intranasal administration. Front Immunol 2023; 14:1166765. [PMID: 37520530 PMCID: PMC10372429 DOI: 10.3389/fimmu.2023.1166765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the danger posed by human coronaviruses. Rapid emergence of immunoevasive variants and waning antiviral immunity decrease the effect of the currently available vaccines, which aim at induction of neutralizing antibodies. In contrast, T cells are marginally affected by antigen evolution although they represent the major mediators of virus control and vaccine protection against virus-induced disease. Materials and methods We generated a multi-epitope vaccine (PanCoVac) that encodes the conserved T cell epitopes from all structural proteins of coronaviruses. PanCoVac contains elements that facilitate efficient processing and presentation of PanCoVac-encoded T cell epitopes and can be uploaded to any available vaccine platform. For proof of principle, we cloned PanCoVac into a non-integrating lentivirus vector (NILV-PanCoVac). We chose Roborovski dwarf hamsters for a first step in evaluating PanCoVac in vivo. Unlike mice, they are naturally susceptible to SARS-CoV-2 infection. Moreover, Roborovski dwarf hamsters develop COVID-19-like disease after infection with SARS-CoV-2 enabling us to look at pathology and clinical symptoms. Results Using HLA-A*0201-restricted reporter T cells and U251 cells expressing a tagged version of PanCoVac, we confirmed in vitro that PanCoVac is processed and presented by HLA-A*0201. As mucosal immunity in the respiratory tract is crucial for protection against respiratory viruses such as SARS-CoV-2, we tested the protective effect of single-low dose of NILV-PanCoVac administered via the intranasal (i.n.) route in the Roborovski dwarf hamster model of COVID-19. After infection with ancestral SARS-CoV-2, animals immunized with a single-low dose of NILV-PanCoVac i.n. did not show symptoms and had significantly decreased viral loads in the lung tissue. This protective effect was observed in the early phase (2 days post infection) after challenge and was not dependent on neutralizing antibodies. Conclusion PanCoVac, a multi-epitope vaccine covering conserved T cell epitopes from all structural proteins of coronaviruses, might protect from severe disease caused by SARS-CoV-2 variants and future pathogenic coronaviruses. The use of (HLA-) humanized animal models will allow for further efficacy studies of PanCoVac-based vaccines in vivo.
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Affiliation(s)
- Mohammed O. Abdelaziz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin J. Raftery
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julian Weihs
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatrics, Division of Gastroenterology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olivia Bielawski
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard Edel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Köppke
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Julia M. Adler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Theresa Firsching
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Luca V. Hummel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivan Fernandez Munoz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francesca Müller-Marquardt
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Partner Site Berlin, Berlin, Germany
| | - Nooran S. Elleboudy
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Günther Schönrich
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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72
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Federico L, Tvedt THA, Gainullin M, Osen JR, Chaban V, Lund KP, Tietze L, Tran TT, Lund-Johansen F, Kared H, Lind A, Vaage JT, Stratford R, Tennøe S, Malone B, Clancy T, Myhre AEL, Gedde-Dahl T, Munthe LA. Robust spike-specific CD4 + and CD8 + T cell responses in SARS-CoV-2 vaccinated hematopoietic cell transplantation recipients: a prospective, cohort study. Front Immunol 2023; 14:1210899. [PMID: 37503339 PMCID: PMC10369799 DOI: 10.3389/fimmu.2023.1210899] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/29/2023] Open
Abstract
Poor overall survival of hematopoietic stem cell transplantation (HSCT) recipients who developed COVID-19 underlies the importance of SARS-CoV-2 vaccination. Previous studies of vaccine efficacy have reported weak humoral responses but conflicting results on T cell immunity. Here, we have examined the relationship between humoral and T cell response in 48 HSCT recipients who received two doses of Moderna's mRNA-1273 or Pfizer/BioNTech's BNT162b2 vaccines. Nearly all HSCT patients had robust T cell immunity regardless of protective humoral responses, with 18/48 (37%, IQR 8.679-5601 BAU/mL) displaying protective IgG anti-receptor binding domain (RBD) levels (>2000 BAU/mL). Flow cytometry analysis of activation induced markers (AIMs) revealed that 90% and 74% of HSCT patients showed reactivity towards immunodominant spike peptides in CD8+ and CD4+ T cells, respectively. The response rate increased to 90% for CD4+ T cells as well when we challenged the cells with a complete set of overlapping peptides spanning the entire spike protein. T cell response was detectable as early as 3 months after transplant, but only CD4+ T cell reactivity correlated with IgG anti-RBD level and time after transplantation. Boosting increased seroconversion rate, while only one patient developed COVID-19 requiring hospitalization. Our data suggest that HSCT recipients with poor serological responses were protected from severe COVID-19 by vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katrine Persgård Lund
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, 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
| | - Trung The Tran
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, 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
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - John Torgils Vaage
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | - Anders Eivind Leren Myhre
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Ludvig André Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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73
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Knell AI, Böhm AK, Jäger M, Kerschbaum J, Engl S, Rudnicki M, Buchwinkler L, Bellmann-Weiler R, Posch W, Weiss G. Virus-Subtype-Specific Cellular and Humoral Immune Response to a COVID-19 mRNA Vaccine in Chronic Kidney Disease Patients and Renal Transplant Recipients. Microorganisms 2023; 11:1756. [PMID: 37512928 PMCID: PMC10383116 DOI: 10.3390/microorganisms11071756] [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: 05/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Patients with chronic kidney disease (CKD) or immunosuppression are at increased risk of severe SARS-CoV-2 infection. The vaccination of CKD patients has resulted in lower antibody concentrations and possibly reduced protection. However, little information is available on how T-cell-mediated immune response is affected in those patients and how vaccine-induced immune responses can neutralise different SARS-CoV-2 variants. Herein, we studied virus-specific humoral and cellular immune responses after two doses of mRNA-1273 (Moderna) vaccine in 42 patients suffering from CKD, small vessel vasculitis (maintenance phase), or kidney transplant recipients (KT). Serum and PBMCs from baseline and at three months after vaccination were used to determine SARS-CoV-2 S1-specific antibodies, neutralisation titers against SARS-CoV-2 WT, B1.617.2 (delta), and BA.1 (omicron) variants as well as virus-specific T-cells via IFNγ ELISpot assays. We observed a significant increase in quantitative and neutralising antibody titers against SARS-CoV-2 and significantly increased T-cell responses to SARS-CoV-2 S1 antigen after vaccination only in the CKD patients. In patients with vasculitis, neither humoral nor cellular responses were detected. In KT recipients, antibodies and virus neutralisation against WT and delta, but not against omicron BA.1, was assured. Importantly, we found no specific SARS-CoV-2 T-cell response in vasculitis and KT subjects, although unspecific T-cell activation was evident in most patients even before vaccination. While pre-dialysis CKD patients appear to mount an effective immune response for in vitro neutralisation of SARS-CoV-2, KT and vasculitis patients under immunosuppressive therapy were insufficiently protected from SARS-CoV-2 two months after the second dose of an mRNA vaccine.
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Affiliation(s)
- Astrid I Knell
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Anna K Böhm
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Julia Kerschbaum
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Sabine Engl
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Lukas Buchwinkler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
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74
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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75
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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76
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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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77
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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of common cold coronaviruses. Cell Rep Med 2023; 4:101088. [PMID: 37295422 PMCID: PMC10242702 DOI: 10.1016/j.xcrm.2023.101088] [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: 12/16/2022] [Revised: 03/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The coronavirus (CoV) family includes several viruses infecting humans, highlighting the importance of exploring pan-CoV vaccine strategies to provide broad adaptive immune protection. We analyze T cell reactivity against representative Alpha (NL63) and Beta (OC43) common cold CoVs (CCCs) in pre-pandemic samples. S, N, M, and nsp3 antigens are immunodominant, as shown for severe acute respiratory syndrome 2 (SARS2), while nsp2 and nsp12 are Alpha or Beta specific. We further identify 78 OC43- and 87 NL63-specific epitopes, and, for a subset of those, we assess the T cell capability to cross-recognize sequences from representative viruses belonging to AlphaCoV, sarbecoCoV, and Beta-non-sarbecoCoV groups. We find T cell cross-reactivity within the Alpha and Beta groups, in 89% of the instances associated with sequence conservation >67%. However, despite conservation, limited cross-reactivity is observed for sarbecoCoV, indicating that previous CoV exposure is a contributing factor in determining cross-reactivity. Overall, these results provide critical insights in developing future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, 16132 Genoa, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
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78
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Tiezzi C, Vecchi A, Rossi M, Cavazzini D, Bolchi A, Laccabue D, Doselli S, Penna A, Sacchelli L, Brillo F, Meschi T, Ticinesi A, Nouvenne A, Donofrio G, Zanelli P, Benecchi M, Giuliodori S, Fisicaro P, Montali I, Ceccatelli Berti C, Reverberi V, Montali A, Urbani S, Pedrazzi G, Missale G, Telenti A, Corti D, Ottonello S, Ferrari C, Boni C. Natural heteroclitic-like peptides are generated by SARS-CoV-2 mutations. iScience 2023; 26:106940. [PMID: 37275517 PMCID: PMC10200277 DOI: 10.1016/j.isci.2023.106940] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Humoral immunity is sensitive to evasion by SARS-CoV-2 mutants, but CD8 T cells seem to be more resistant to mutational inactivation. By a systematic analysis of 30 spike variant peptides containing the most relevant VOC and VOI mutations that have accumulated overtime, we show that in vaccinated and convalescent subjects, mutated epitopes can have not only a neutral or inhibitory effect on CD8 T cell recognition but can also enhance or generate de novo CD8 T cell responses. The emergence of these mutated T cell function enhancing epitopes likely reflects an epiphenomenon of SARS-CoV-2 evolution driven by antibody evasion and increased virus transmissibility. In a subset of individuals with weak and narrowly focused CD8 T cell responses selection of these heteroclitic-like epitopes may bear clinical relevance by improving antiviral protection. The functional enhancing effect of these peptides is also worth of consideration for the future development of new generation, more potent COVID-19 vaccines.
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Affiliation(s)
- Camilla Tiezzi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Andrea Vecchi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Marzia Rossi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Angelo Bolchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Center Biopharmanet-Tec, University of Parma, Parma, Italy
| | - Diletta Laccabue
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Sara Doselli
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Amalia Penna
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Luca Sacchelli
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Federica Brillo
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Gaetano Donofrio
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Paola Zanelli
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Magda Benecchi
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Silvia Giuliodori
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Paola Fisicaro
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Ilaria Montali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Valentina Reverberi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Anna Montali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Urbani
- UO Immunoematologia e Medicina Trasfusionale, Dipartimento Diagnostico, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Giuseppe Pedrazzi
- Department of Neuroscience - Biophysics and Medical Physics Unit, University of Parma, Parma, Italy
| | - Gabriele Missale
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Simone Ottonello
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Center Biopharmanet-Tec, University of Parma, Parma, Italy
| | - Carlo Ferrari
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Carolina Boni
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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79
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Ansari M, White AD. Learning Peptide Properties with Positive Examples Only. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543289. [PMID: 37333233 PMCID: PMC10274696 DOI: 10.1101/2023.06.01.543289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Deep learning can create accurate predictive models by exploiting existing large-scale experimental data, and guide the design of molecules. However, a major barrier is the requirement of both positive and negative examples in the classical supervised learning frameworks. Notably, most peptide databases come with missing information and low number of observations on negative examples, as such sequences are hard to obtain using high-throughput screening methods. To address this challenge, we solely exploit the limited known positive examples in a semi-supervised setting, and discover peptide sequences that are likely to map to certain antimicrobial properties via positive-unlabeled learning (PU). In particular, we use the two learning strategies of adapting base classifier and reliable negative identification to build deep learning models for inferring solubility, hemolysis, binding against SHP-2, and non-fouling activity of peptides, given their sequence. We evaluate the predictive performance of our PU learning method and show that by only using the positive data, it can achieve competitive performance when compared with the classical positive-negative (PN) classification approach, where there is access to both positive and negative examples.
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Affiliation(s)
- Mehrad Ansari
- Department of Chemical Engineering, University of Rochester, Rochester, NY, 14627, USA
| | - Andrew D. White
- Department of Chemical Engineering, University of Rochester, Rochester, NY, 14627, USA
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80
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Nguyen CM, Luong BA, Thi Tran TT, Nguyen HN, Tran LS. Design and generation of mRNAs encoding conserved regions of SARS-CoV-2 ORF1ab for T cell-mediated immune activation. Future Virol 2023; 18:501-516. [PMID: 38051989 PMCID: PMC10308627 DOI: 10.2217/fvl-2023-0066] [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: 03/24/2023] [Accepted: 06/13/2023] [Indexed: 12/07/2023]
Abstract
Aim To generate mRNAs encoding conserved regions within SARS-CoV-2 ORF1ab which can induce strong T-cell responses to overcome the immune invasion of newly emergent variants. Methods We selected two conserved regions with a high density of T-cell epitopes using immunoinformatics for mRNA synthesis. The ability of testing mRNAs to activate T cells for IFN-γ production was examined by an ELISpot assay and flow cytometry. Results Two synthesized mRNAs were successfully translated in MDA-MB-231 cells and had comparable potency to the spike mRNA to induce CD4+ and CD8+ T-cell responses in peripheral blood mononuclear cells in 29 out of 34 participants. Conclusion This study provides a proof-of-concept for the use of SARS-CoV-2 conserved regions to develop booster vaccines capable of eliciting T-cell-mediated immunity.
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Affiliation(s)
| | - Bac An Luong
- University of Medicine & Pharmacy at Ho Chi Minh City, Vietnam
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81
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Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542482. [PMID: 37398281 PMCID: PMC10312465 DOI: 10.1101/2023.05.26.542482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I landscape, here we report viral peptides that are naturally processed and loaded onto HLA-II complexes in infected cells. We identified over 500 unique viral peptides from canonical proteins, as well as from overlapping internal open reading frames (ORFs), revealing, for the first time, the contribution of internal ORFs to the HLA-II peptide repertoire. Most HLA-II peptides co-localized with the known CD4+ T cell epitopes in COVID-19 patients. We also observed that two reported immunodominant regions in the SARS-CoV-2 membrane protein are formed at the level of HLA-II presentation. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and non-structural and non-canonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize the vaccine effectiveness.
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82
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Yunis J, Short KR, Yu D. Severe respiratory viral infections: T-cell functions diverging from immunity to inflammation. Trends Microbiol 2023; 31:644-656. [PMID: 36635162 PMCID: PMC9829516 DOI: 10.1016/j.tim.2022.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023]
Abstract
Respiratory viral infections such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV) trigger distinct clinical outcomes defined by immunity-based viral clearance or disease associated with exaggerated and prolonged inflammation. The important role of T cells in shaping both antiviral immunity and inflammation has revived interest in understanding the host-pathogen interactions that lead to the diverse functions of T cells in respiratory viral infections. Inborn deficiencies and acquired insufficiency in immunity can prolong infection and shift the immune response towards exacerbated inflammation, which results from persistent innate immune activation and bystander T-cell activation that is nonspecific to the pathogen but is often driven by cytokines. This review discusses how virus variants, exposure doses, routes of infection, host genetics, and immune history can modulate the activation and function of T cells, thus influencing clinical outcomes. Knowledge of virus-host interaction can inform strategies to prevent immune dysfunction in respiratory viral infection and help in the treatment of associated diseases.
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Affiliation(s)
- Joseph Yunis
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
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83
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Brisotto G, Montico M, Turetta M, Zanussi S, Cozzi MR, Vettori R, Boschian Boschin R, Vinante L, Matrone F, Revelant A, Palazzari E, Innocente R, Fanetti G, Gerratana L, Garutti M, Lisanti C, Bolzonello S, Nicoloso MS, Steffan A, Muraro E. Integration of Cellular and Humoral Immune Responses as an Immunomonitoring Tool for SARS-CoV-2 Vaccination in Healthy and Fragile Subjects. Viruses 2023; 15:1276. [PMID: 37376576 DOI: 10.3390/v15061276] [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: 05/12/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular and humoral immunity are both required for SARS-CoV-2 infection recovery and vaccine efficacy. The factors affecting mRNA vaccination-induced immune responses, in healthy and fragile subjects, are still under investigation. Thus, we monitored the vaccine-induced cellular and humoral immunity in healthy subjects and cancer patients after vaccination to define whether a different antibody titer reflected similar rates of cellular immune responses and if cancer has an impact on vaccination efficacy. We found that higher titers of antibodies were associated with a higher probability of positive cellular immunity and that this greater immune response was correlated with an increased number of vaccination side effects. Moreover, active T-cell immunity after vaccination was associated with reduced antibody decay. The vaccine-induced cellular immunity appeared more likely in healthy subjects rather than in cancer patients. Lastly, after boosting, we observed a cellular immune conversion in 20% of subjects, and a strong correlation between pre- and post-boosting IFN-γ levels, while antibody levels did not display a similar association. Finally, our data suggested that integrating humoral and cellular immune responses could allow the identification of SARS-CoV-2 vaccine responders and that T-cell responses seem more stable over time compared to antibodies, especially in cancer patients.
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Affiliation(s)
- Giulia Brisotto
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Marcella Montico
- Clinical Trial Office, Scientific Direction, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Matteo Turetta
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Stefania Zanussi
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Maria Rita Cozzi
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Roberto Vettori
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Romina Boschian Boschin
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Lorenzo Vinante
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Fabio Matrone
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Alberto Revelant
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Elisa Palazzari
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Roberto Innocente
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Giuseppe Fanetti
- Division of Radiation Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Lorenzo Gerratana
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Mattia Garutti
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Camilla Lisanti
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Silvia Bolzonello
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Milena Sabrina Nicoloso
- Molecular Oncology Unit, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Elena Muraro
- Immunopathology and Cancer Biomarkers Units, Department of Cancer Research and Advanced Diagnostics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
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84
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Arieta CM, Xie YJ, Rothenberg DA, Diao H, Harjanto D, Meda S, Marquart K, Koenitzer B, Sciuto TE, Lobo A, Zuiani A, Krumm SA, Cadima Couto CI, Hein S, Heinen AP, Ziegenhals T, Liu-Lupo Y, Vogel AB, Srouji JR, Fesser S, Thanki K, Walzer K, Addona TA, Türeci Ö, Şahin U, Gaynor RB, Poran A. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Cell 2023; 186:2392-2409.e21. [PMID: 37164012 PMCID: PMC10099181 DOI: 10.1016/j.cell.2023.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/12/2023] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
T cell responses play an important role in protection against beta-coronavirus infections, including SARS-CoV-2, where they associate with decreased COVID-19 disease severity and duration. To enhance T cell immunity across epitopes infrequently altered in SARS-CoV-2 variants, we designed BNT162b4, an mRNA vaccine component that is intended to be combined with BNT162b2, the spike-protein-encoding vaccine. BNT162b4 encodes variant-conserved, immunogenic segments of the SARS-CoV-2 nucleocapsid, membrane, and ORF1ab proteins, targeting diverse HLA alleles. BNT162b4 elicits polyfunctional CD4+ and CD8+ T cell responses to diverse epitopes in animal models, alone or when co-administered with BNT162b2 while preserving spike-specific immunity. Importantly, we demonstrate that BNT162b4 protects hamsters from severe disease and reduces viral titers following challenge with viral variants. These data suggest that a combination of BNT162b2 and BNT162b4 could reduce COVID-19 disease severity and duration caused by circulating or future variants. BNT162b4 is currently being clinically evaluated in combination with the BA.4/BA.5 Omicron-updated bivalent BNT162b2 (NCT05541861).
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Affiliation(s)
| | - Yushu Joy Xie
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | - Huitian Diao
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Dewi Harjanto
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Shirisha Meda
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Adam Zuiani
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | - John R Srouji
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Özlem Türeci
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Uğur Şahin
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany
| | | | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA.
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85
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Benede NSB, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Mennen M, Skelem S, Adriaanse M, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, Botha M, Workman L, Zar HJ, Ntusi NAB, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290059. [PMID: 37292954 PMCID: PMC10246143 DOI: 10.1101/2023.05.16.23290059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi S. B. Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A. B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
- Crick African Network, The Francis Crick Institute, London, United Kingdom
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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86
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Chour W, Choi J, Xie J, Chaffee ME, Schmitt TM, Finton K, DeLucia DC, Xu AM, Su Y, Chen DG, Zhang R, Yuan D, Hong S, Ng AHC, Butler JZ, Edmark RA, Jones LC, Murray KM, Peng S, Li G, Strong RK, Lee JK, Goldman JD, Greenberg PD, Heath JR. Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis. Commun Biol 2023; 6:528. [PMID: 37193826 PMCID: PMC10186326 DOI: 10.1038/s42003-023-04899-8] [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: 11/08/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
The discovery and characterization of antigen-specific CD8+ T cell clonotypes typically involves the labor-intensive synthesis and construction of peptide-MHC tetramers. We adapt single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation, showing that hundreds can be rapidly prepared across multiple Class I HLA alleles. We use this platform to explore the impact of peptide and SCT template mutations on protein expression yield, thermal stability, and functionality. SCT libraries were an efficient tool for identifying T cells recognizing commonly reported viral epitopes. We then construct SCT libraries to capture SARS-CoV-2 specific CD8+ T cells from COVID-19 participants and healthy donors. The immunogenicity of these epitopes is validated by functional assays of T cells with cloned TCRs captured using SCT libraries. These technologies should enable the rapid analyses of peptide-based T cell responses across several contexts, including autoimmunity, cancer, or infectious disease.
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Affiliation(s)
- William Chour
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Mary E Chaffee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kathryn Finton
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander M Xu
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Daniel G Chen
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Microbiology and Department of Informatics, University of Washington, Seattle, WA, 98195, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Alphonsus H C Ng
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonah Z Butler
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rick A Edmark
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Kim M Murray
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Guideng Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Key Laboratory of Synthetic Biology Regulatory Element, Chinese Academy of Medical Sciences, Beijing, China
| | - Roland K Strong
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, 98104, USA
- Division of Infectious Disease, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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87
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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88
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Song K, Xu H, Da LT. Loading dynamics of one SARS-CoV-2-derived peptide into MHC-II revealed by kinetic models. Biophys J 2023; 122:1665-1677. [PMID: 36964657 PMCID: PMC10036144 DOI: 10.1016/j.bpj.2023.03.032] [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: 06/18/2022] [Revised: 11/24/2022] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
Major histocompatibility complex class II (MHC-II) plays an indispensable role in activating CD4+ T cell immune responses by presenting antigenic peptides on the cell surface for recognition by T cell receptors. The assembly of MHC-II and antigenic peptide is therefore a prerequisite for the antigen presentation. To date, however, the atomic-level mechanism underlying the peptide-loading dynamics for MHC-II is still elusive. Here, by constructing Markov state models based on extensive all-atom molecular dynamics simulations, we reveal the complete peptide-loading dynamics into MHC-II for one SARS-CoV-2 S-protein-derived antigenic peptide (235ITRFQTLLALHRSYL249). Our Markov state model identifies six metastable states (S1-S6) during the peptide-loading process and determines two dominant loading pathways. The peptide could potentially approach the antigen-binding groove via either its N- or C-terminus. Then, the consecutive insertion of several anchor residues into the binding pockets profoundly dictates the peptide-loading dynamics. Notably, the MHC-II αA52-E55 motif could guide the peptide loading into the antigen-binding groove via forming β-sheets conformation with the incoming peptide. The rate-limiting step, namely S5→S6, is mainly attributed to a considerable desolvation penalty triggered by the binding of the peptide C-terminus. Moreover, we further examined the conformational changes associated with the peptide exchange process catalyzed by the chaperon protein HLA-DM. A flipped-out conformation of MHC-II αW43 captured in S1-S3 is considered a critical anchor point for HLA-DM to modulate the structural dynamics. Our work provides deep structural insights into the key regulatory factors in MHC-II responsible for peptide recognition and guides future design for peptide vaccines against SARS-CoV-2.
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Affiliation(s)
- Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Honglin Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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89
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Oh S, Seo H. Dietary intervention with functional foods modulating gut microbiota for improving the efficacy of COVID-19 vaccines. Heliyon 2023; 9:e15668. [PMID: 37124341 PMCID: PMC10121067 DOI: 10.1016/j.heliyon.2023.e15668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
Dysbiosis of the gut microbiota with aging contributes to a reduction in important cross-feeding bacterial reactions in the gut and immunosenescence, which could contribute to a decrease in vaccine efficacy. Fever, cough, and fatigue are the main signs of coronavirus disease 2019 (COVID-19); however, some patients with COVID-19 present with gastrointestinal symptoms. COVID-19 vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the best measures to reduce SARS-CoV-2 infection rates and the severity of COVID-19. The immunogenicity of COVID-19 vaccines is influenced by the composition of the gut microbiota, and the immune response to COVID-19 vaccines decreases with age. In this review, we discuss gut microbiota dysbiosis and immunosenescence in the older adults, the role of gut microbiota in improving the efficacy of COVID-19 vaccines, and dietary interventions to improve the efficacy of COVID-19 vaccines in the older adults.
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Affiliation(s)
- Soyoung Oh
- Infectious Disease Research Center, Citizen's Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul, 04524, Republic of Korea
| | - Haesook Seo
- Infectious Disease Research Center, Citizen's Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul, 04524, Republic of Korea
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90
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Murray SM, Ansari AM, Frater J, Klenerman P, Dunachie S, Barnes E, Ogbe A. The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses. Nat Rev Immunol 2023; 23:304-316. [PMID: 36539527 PMCID: PMC9765363 DOI: 10.1038/s41577-022-00809-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.
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Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Azim M Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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91
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Adams LE, Leist SR, Dinnon KH, West A, Gully KL, Anderson EJ, Loome JF, Madden EA, Powers JM, Schäfer A, Sarkar S, Castillo IN, Maron JS, McNamara RP, Bertera HL, Zweigert MR, Higgins JS, Hampton BK, Premkumar L, Alter G, Montgomery SA, Baxter VK, Heise MT, Baric RS. Fc-mediated pan-sarbecovirus protection after alphavirus vector vaccination. Cell Rep 2023; 42:112326. [PMID: 37000623 PMCID: PMC10063157 DOI: 10.1016/j.celrep.2023.112326] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
Group 2B β-coronaviruses (sarbecoviruses) have caused regional and global epidemics in modern history. Here, we evaluate the mechanisms of cross-sarbecovirus protective immunity, currently less clear yet important for pan-sarbecovirus vaccine development, using a panel of alphavirus-vectored vaccines covering bat to human strains. While vaccination does not prevent virus replication, it protects against lethal heterologous disease outcomes in both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and clade 2 bat sarbecovirus challenge models. The spike vaccines tested primarily elicit a highly S1-specific homologous neutralizing antibody response with no detectable cross-virus neutralization. Rather, non-neutralizing antibody functions, mechanistically linked to FcgR4 and spike S2, mediate cross-protection in wild-type mice. Protection is lost in FcR knockout mice, further supporting a model for non-neutralizing, protective antibodies. These data highlight the importance of FcR-mediated cross-protective immune responses in universal pan-sarbecovirus vaccine designs.
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Affiliation(s)
- Lily E Adams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth J Anderson
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer F Loome
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Madden
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Izabella N Castillo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jenny S Maron
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Harry L Bertera
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Mark R Zweigert
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jaclyn S Higgins
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Dallas Tissue Research, Dallas, TX, USA
| | - Victoria K Baxter
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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92
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Chen F, Huang Y, Huang Z, Jiang T, Yang Z, Zeng J, Jin A, Zuo H, Huang CZ, Mao C. DNA-scaffolded multivalent vaccine against SARS-CoV-2. Acta Biomater 2023; 164:387-396. [PMID: 37088158 PMCID: PMC10122553 DOI: 10.1016/j.actbio.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
Short peptides are poor immunogens. One way to increase their immune responses is by arraying immunogens in multivalency. Simple and efficient scaffolds for spatial controlling the inter-antigen distance and enhancing immune activation are required. Here, we report a molecular vaccine design principle that maximally drives potent SARS-CoV-2 RBD subunit vaccine on DNA duplex to induce robust and efficacious immune responses in vivo. We expect that the DNA-peptide epitope platform represents a facile and generalizable strategy to enhance the immune response. STATEMENT OF SIGNIFICANCE: DNA scaffolds offer a biocompatible and convenient platform for arraying immunogens in multivalency antigenic peptides, and spatially control the inter-antigen distance. This can effectively enhance immune response. Peptide (instead of entire protein) vaccines are highly attractive. However, short peptides are poor immunogens. Our DNA scaffolded multivalent peptide immunogen system induced robust and efficacious immune response in vivo as demonstrated by the antigenic peptide against SAR-CoV-2. The present strategy could be readily generalized and adapted to prepare multivalent vaccines against other viruses or disease. Particularly, the different antigens could be integrated into one single vaccine and lead to super-vaccines that can protect the host from multiple different viruses or multiple variants of the same virus.
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Affiliation(s)
- Fangfang Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuhan Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhengyu Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Tingting Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zailin Yang
- Department of Hematology-Oncology, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Jie Zeng
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; Department of Chemistry, Purdue University, West Lafayette 47907, IN, USA.
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93
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Pereira SM, Barreto FR, de Souza RA, de Souza Teles Santos CA, Pereira M, da Paixão ES, de Jesus Lima CCO, da Natividade MS, Lindoso AABP, Fernandes EG, Junior EBC, Pescarini JM, de Andrade KVF, de Souza FM, de Britto EA, Nunes C, Ichihara MY, Dalcolmo M, Trajman A, Barral-Netto M, Abubakar I, Barreto ML, de Alencar Ximenes RA, Rodrigues LC. Previous BCG vaccination is associated with less severe clinical progression of COVID-19. BMC Med 2023; 21:145. [PMID: 37055776 PMCID: PMC10099006 DOI: 10.1186/s12916-023-02859-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND BCG vaccination, originally used to prevent tuberculosis, is known to "train" the immune system to improve defence against viral respiratory infections. We investigated whether a previous BCG vaccination is associated with less severe clinical progression of COVID-19 METHODS: A case-control study comparing the proportion with a BCG vaccine scar (indicating previous vaccination) in cases and controls presenting with COVID-19 to health units in Brazil. Cases were subjects with severe COVID-19 (O2 saturation < 90%, severe respiratory effort, severe pneumonia, severe acute respiratory syndrome, sepsis, and septic shock). Controls had COVID-19 not meeting the definition of "severe" above. Unconditional regression was used to estimate vaccine protection against clinical progression to severe disease, with strict control for age, comorbidity, sex, educational level, race/colour, and municipality. Internal matching and conditional regression were used for sensitivity analysis. RESULTS BCG was associated with high protection against COVID-19 clinical progression, over 87% (95% CI 74-93%) in subjects aged 60 or less and 35% (95% CI - 44-71%) in older subjects. CONCLUSIONS This protection may be relevant for public health in settings where COVID-19 vaccine coverage is still low and may have implications for research to identify vaccine candidates for COVID-19 that are broadly protective against mortality from future variants. Further research into the immunomodulatory effects of BCG may inform COVID-19 therapeutic research.
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Affiliation(s)
| | | | | | - Carlos Antonio de Souza Teles Santos
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
- Department of Exact Sciences, State University of Feira de Santana, Bahia, Salvador, Brazil
| | - Marcos Pereira
- Institute of Collective Health, Federal University of Bahia, Salvador, Brazil.
| | - Enny Santos da Paixão
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
- Faculty of Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | | | | | - Julia Moreira Pescarini
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
- Faculty of Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Elisangela Alves de Britto
- Institute of Collective Health, Federal University of Bahia, Salvador, Brazil
- State Department of Health of Bahia, Institute Couto Maia, Salvador, Brazil
| | - Ceuci Nunes
- State Department of Health of Bahia, Institute Couto Maia, Salvador, Brazil
| | - Maria Yuri Ichihara
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
| | - Margareth Dalcolmo
- Hélio Fraga Reference Center, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Anete Trajman
- Departamento de Clínica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- McGill TB International Centre, McGill University, Montreal, Canada
| | - Manoel Barral-Netto
- Institute Gonçalo Moniz - Fundação Oswaldo Cruz (Fiocruz), Salvador, Brazil
- Faculdade de Medicina, Federal University of Bahia, Salvador, Brazil
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Mauricio Lima Barreto
- Institute of Collective Health, Federal University of Bahia, Salvador, Brazil
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
| | | | - Laura Cunha Rodrigues
- Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
- Faculty of Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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94
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Tada T, Peng JY, Dcosta BM, Landau NR. Single-epitope T cell-based vaccine protects against SARS-CoV-2 infection in a preclinical animal model. JCI Insight 2023; 8:167306. [PMID: 37036004 PMCID: PMC10132166 DOI: 10.1172/jci.insight.167306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/21/2023] [Indexed: 04/11/2023] Open
Abstract
Currently authorized COVID-19 vaccines induce humoral and cellular responses to epitopes in the SARS-CoV-2 spike protein, though the relative roles of antibodies and T cells in protection are not well understood. To understand the role of vaccine-elicited T cell responses in protection, we established a T cell-only vaccine using a DC-targeted lentiviral vector expressing single CD8+ T cell epitopes of the viral nucleocapsid, spike, and ORF1. Immunization of angiotensin-converting enzyme 2-transgenic mice with ex vivo lentiviral vector-transduced DCs or by direct injection of the vector induced the proliferation of functional antigen-specific CD8+ T cells, resulting in a 3-log decrease in virus load upon live virus challenge that was effective against the ancestral virus and Omicron variants. The Pfizer/BNT162b2 vaccine was also protective in mice, but the antibodies elicited did not cross-react on the Omicron variants, suggesting that the protection was mediated by T cells. The studies suggest that the T cell response plays an important role in vaccine protection. The findings suggest that the incorporation of additional T cell epitopes into current vaccines would increase their effectiveness and broaden protection.
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95
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MH, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2023; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042 RENNES Cedex, France
| | - Nicolle H. Packer
- Macquarie University, Sydney, NSW 2109, Australia
- Griffith University’s Institute for Glycomics, Sydney, NSW 2109, Australia
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Michael H.A. Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States
| | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou 310024, Zhejiang Province, China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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96
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Hansen L, Brokstad KA, Bansal A, Zhou F, Bredholt G, Onyango TB, Sandnes HH, Elyanow R, Madsen A, Trieu MC, Sævik M, Søyland H, Olofsson JS, Vahokoski J, Ertesvåg NU, Fjelltveit EB, Shafiani S, Tøndel C, Chapman H, Kaplan I, Mohn KG, Langeland N, Cox RJ. Durable immune responses after BNT162b2 vaccination in home-dwelling old adults. Vaccine X 2023; 13:100262. [PMID: 36643855 PMCID: PMC9830931 DOI: 10.1016/j.jvacx.2023.100262] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Objectives Elderly are an understudied, high-risk group vulnerable to severe COVID-19. We comprehensively analyzed the durability of humoral and cellular immune responses after BNT162b2 vaccination and SARS-CoV-2 infection in elderly and younger adults. Methods Home-dwelling old (n = 100, median 86 years) and younger adults (n = 449, median 38 years) were vaccinated with two doses of BNT162b2 vaccine at 3-week intervals and followed for 9-months. Vaccine-induced responses were compared to home-isolated COVID-19 patients (n = 183, median 47 years). Our analysis included neutralizing antibodies, spike-specific IgG, memory B-cells, IFN-γ and IL-2 secreting T-cells and sequencing of the T-cell receptor (TCR) repertoire. Results Spike-specific breadth and depth of the CD4+ and CD8+ TCR repertoires were significantly lower in the elderly after one and two vaccinations. Both vaccinations boosted IFN-γ and IL-2 secreting spike-specific T-cells responses, with 96 % of the elderly and 100 % of the younger adults responding after the second dose, although responses were not maintained at 9-months. In contrast, T-cell responses persisted up to 12-months in infected patients. Spike-specific memory B-cells were induced after the first dose in 87 % of the younger adults compared to 38 % of the elderly, which increased to 83 % after the second dose. Memory B-cells were maintained at 9-months post-vaccination in both vaccination groups. Neutralizing antibody titers were estimated to last for 1-year in younger adults but only 6-months in the older vaccinees. Interestingly, infected older patients (n = 15, median 75 years) had more durable neutralizing titers estimated to last 14-months, 8-months longer than the older vaccinees. Conclusions Vaccine-induced spike-specific IgG and neutralizing antibodies were consistently lower in the older than younger vaccinees. Overall, our data provide valuable insights into the kinetics of the humoral and cellular immune response in the elderly after SARS-CoV-2 vaccination or infection, highlighting the need for two doses, which can guide future vaccine design.Clinical trials.gov; NCT04706390.
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Affiliation(s)
- Lena Hansen
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karl Albert Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Amit Bansal
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Geir Bredholt
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | | | - Anders Madsen
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Mai-Chi Trieu
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marianne Sævik
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hanne Søyland
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jan Stefan Olofsson
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Juha Vahokoski
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nina Urke Ertesvåg
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | - Camilla Tøndel
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
- Department of Research and Innovation, Haukeland University Hospital, Bergen, Norway
| | | | - Ian Kaplan
- Adaptive Biotechnologies, Seattle, WA, USA
| | - Kristin G.I. Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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97
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Wu D, Efimov GA, Bogolyubova AV, Pierce BG, Mariuzza RA. Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor diversity. J Biol Chem 2023; 299:103035. [PMID: 36806685 PMCID: PMC9934920 DOI: 10.1016/j.jbc.2023.103035] [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: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
T cells play a crucial role in combatting SARS-CoV-2 and forming long-term memory responses to this coronavirus. The emergence of SARS-CoV-2 variants that can evade T cell immunity has raised concerns about vaccine efficacy and the risk of reinfection. Some SARS-CoV-2 T cell epitopes elicit clonally restricted CD8+ T cell responses characterized by T cell receptors (TCRs) that lack structural diversity. Mutations in such epitopes can lead to loss of recognition by most T cells specific for that epitope, facilitating viral escape. Here, we studied an HLA-A2-restricted spike protein epitope (RLQ) that elicits CD8+ T cell responses in COVID-19 convalescent patients characterized by highly diverse TCRs. We previously reported the structure of an RLQ-specific TCR (RLQ3) with greatly reduced recognition of the most common natural variant of the RLQ epitope (T1006I). Opposite to RLQ3, TCR RLQ7 recognizes T1006I with even higher functional avidity than the WT epitope. To explain the ability of RLQ7, but not RLQ3, to tolerate the T1006I mutation, we determined structures of RLQ7 bound to RLQ-HLA-A2 and T1006I-HLA-A2. These complexes show that there are multiple structural solutions to recognizing RLQ and thereby generating a clonally diverse T cell response to this epitope that assures protection against viral escape and T cell clonal loss.
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Affiliation(s)
- Daichao Wu
- Laboratory of Structural Immunology, Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China; W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | | | | | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA.
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98
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Purbey PK, Roy K, Gupta S, Paul MK. Mechanistic insight into the protective and pathogenic immune-responses against SARS-CoV-2. Mol Immunol 2023; 156:111-126. [PMID: 36921486 PMCID: PMC10009586 DOI: 10.1016/j.molimm.2023.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
COVID-19 is a severe respiratory illness that has emerged as a devasting health problem worldwide. The disease outcome is heterogeneous, which is most likely dependent on the immunity of an individual. Asymptomatic and mildly/moderate symptomatic (non-severe) patients likely develop an effective early immune response and clear the virus. However, severe symptoms dominate due to a failure in the generation of an effective and specific early immune response against SARS-CoV-2. Moreover, a late surge in pathogenic inflammation involves dysregulated innate and adaptive immune responses leading to local and systemic tissue damage and the emergence of severe disease symptoms. In this review, we describe the potential mechanisms of protective and pathogenic immune responses in "mild/moderate" and "severe" symptomatic SARS-CoV-2 infected people, respectively, and discuss the immune components that are currently targeted for therapeutic intervention.
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Affiliation(s)
- Prabhat K Purbey
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA.
| | - Koushik Roy
- Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Sandeep Gupta
- Department of Neurobiology, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Manash K Paul
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA; Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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99
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Wolday D, Fung CYJ, Morgan G, Casalino S, Frangione E, Taher J, Lerner-Ellis JP. HLA Variation and SARS-CoV-2 Specific Antibody Response. Viruses 2023; 15:906. [PMID: 37112884 PMCID: PMC10143129 DOI: 10.3390/v15040906] [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: 03/15/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Differences in SARS-CoV-2-specific immune responses have been observed between individuals following natural infection or vaccination. In addition to already known factors, such as age, sex, COVID-19 severity, comorbidity, vaccination status, hybrid immunity, and duration of infection, inter-individual variations in SARS-CoV-2 immune responses may, in part, be explained by structural differences brought about by genetic variation in the human leukocyte antigen (HLA) molecules responsible for the presentation of SARS-CoV-2 antigens to T effector cells. While dendritic cells present peptides with HLA class I molecules to CD8+ T cells to induce cytotoxic T lymphocyte responses (CTLs), they present peptides with HLA class II molecules to T follicular helper cells to induce B cell differentiation followed by memory B cell and plasma cell maturation. Plasma cells then produce SARS-CoV-2-specific antibodies. Here, we review published data linking HLA genetic variation or polymorphisms with differences in SARS-CoV-2-specific antibody responses. While there is evidence that heterogeneity in antibody response might be related to HLA variation, there are conflicting findings due in part to differences in study designs. We provide insight into why more research is needed in this area. Elucidating the genetic basis of variability in the SARS-CoV-2 immune response will help to optimize diagnostic tools and lead to the development of new vaccines and therapeutics against SARS-CoV-2 and other infectious diseases.
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Affiliation(s)
- Dawit Wolday
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Chun Yiu Jordan Fung
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Gregory Morgan
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Selina Casalino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Erika Frangione
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Jennifer Taher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Jordan P. Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
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100
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Harne R, Williams B, Abdelaal HFM, Baldwin SL, Coler RN. SARS-CoV-2 infection and immune responses. AIMS Microbiol 2023; 9:245-276. [PMID: 37091818 PMCID: PMC10113164 DOI: 10.3934/microbiol.2023015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
The recent pandemic caused by the SARS-CoV-2 virus continues to be an enormous global challenge faced by the healthcare sector. Availability of new vaccines and drugs targeting SARS-CoV-2 and sequelae of COVID-19 has given the world hope in ending the pandemic. However, the emergence of mutations in the SARS-CoV-2 viral genome every couple of months in different parts of world is a persistent danger to public health. Currently there is no single treatment to eradicate the risk of COVID-19. The widespread transmission of SARS-CoV-2 due to the Omicron variant necessitates continued work on the development and implementation of effective vaccines. Moreover, there is evidence that mutations in the receptor domain of the SARS-CoV-2 spike glycoprotein led to the decrease in current vaccine efficacy by escaping antibody recognition. Therefore, it is essential to actively identify the mechanisms by which SARS-CoV-2 evades the host immune system, study the long-lasting effects of COVID-19 and develop therapeutics targeting SARS-CoV-2 infections in humans and preclinical models. In this review, we describe the pathogenic mechanisms of SARS-CoV-2 infection as well as the innate and adaptive host immune responses to infection. We address the ongoing need to develop effective vaccines that provide protection against different variants of SARS-CoV-2, as well as validated endpoint assays to evaluate the immunogenicity of vaccines in the pipeline, medications, anti-viral drug therapies and public health measures, that will be required to successfully end the COVID-19 pandemic.
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Affiliation(s)
- Rakhi Harne
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Brittany Williams
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Hazem F. M. Abdelaal
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Susan L. Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Rhea N. Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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