351
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Mahmud S, Paul GK, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Hossain A, Promi MM, Ema FK, Chidambaram K, Chandrasekaran B, Alqahtani AM, Emran TB, Saleh MA. Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2. Front Mol Biosci 2021; 8:628585. [PMID: 34041263 PMCID: PMC8142691 DOI: 10.3389/fmolb.2021.628585] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Fahmida Khan Ema
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Balakumar Chandrasekaran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Philadelphia University-Jordan, Amman, Jordan
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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352
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Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman A, Jehi L, Mayadas TN. Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.03.441323. [PMID: 33972940 PMCID: PMC8109200 DOI: 10.1101/2021.05.03.441323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells are critical for control of viral infection and effective vaccination. We investigated whether prior Measles-Mumps-Rubella (MMR) or Tetanus-Diphtheria-pertussis (Tdap) vaccination elicit cross-reactive T cells that mitigate COVID-19. Using co-cultures of antigen presenting cells (APC) loaded with antigens and autologous T cells, we found a high correlation between responses to SARS-CoV-2 (Spike-S1 and Nucleocapsid) and MMR and Tdap vaccine proteins in both SARS-CoV-2 infected individuals and individuals immunized with mRNA-based SARS-CoV-2 vaccines. The overlapping T cell population contained effector memory T cells (TEMRA) previously implicated in anti-viral immunity and their activation required APC-derived IL-15. TCR- and scRNA-sequencing detected cross-reactive clones with TEMRA features among the cells recognizing SARS-CoV-2, MMR and Tdap epitopes. A propensity-weighted analysis of 73,582 COVID-19 patients revealed that severe disease outcomes (hospitalization and transfer to intensive care unit or death) were reduced in MMR or Tdap vaccinated individuals by 38-32% and 23-20% respectively. In summary, SARS-CoV-2 re-activates memory T cells generated by Tdap and MMR vaccines, which may reduce disease severity.
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353
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Esmaeili S, Abbasi MH, Abolmaali M, Mojtahed M, Alavi SNR, Soleimani S, Mokhtari M, Hatam J, Khotbehsara ST, Motamed MR, Joghataei MT, Mirzaasgari Z, Moghaddasi M. Rituximab and risk of COVID-19 infection and its severity in patients with MS and NMOSD. BMC Neurol 2021; 21:183. [PMID: 33933026 PMCID: PMC8087518 DOI: 10.1186/s12883-021-02218-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Choosing a safe disease modifying therapy during the COVID-19 pandemic is challenging. This case series study was conducted to determine the incidence rate and the course of Covid-19 infection in MS/NMOSD patients treated with Rituximab. METHODS In this study, we designed a web-based questionnaire. Baseline information such as patient- reported walking disability, total number of Rituximab infusions received, delayed injections, occurrence of any relapse, and the use of corticosteroids during the pandemic were collected. Also, information regarding the Covid-19 pandemic such as adherence to self-isolation, any recent exposure to an infected individual and the presence of suggestive symptoms were collected. In case of positive test results, patients were grouped into 2 categories; mild to moderate and seriously ill and outcomes were evaluated as favorable (improved/ discharged) and unfavorable (expired). RESULTS Two hundred fifty-eight patients with Multiple Sclerosis were enrolled in this study, 9 of the subjects (3.4%) were confirmed positive for Covid-19, five of which required hospitalizations (55.5%), two patients required ICU admission (22.2%) and 2 two patients died (22.2%). None of these patients ever mentioned using corticosteroids during the pandemic. In comparison to MS patients who were not receiving disease modifying therapy (DMT), our study indicated a higher incidence of Covid-19 infection, higher ratio of serious illness and a higher fatality ratio. CONCLUSIONS Rituximab seems not to be safe enough during the pandemic.
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Affiliation(s)
- Sara Esmaeili
- Cellular and Molecular Research Center, Iran university of medical sciences, Tehran, Iran
- School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Abbasi
- Cellular and Molecular Research Center, Iran university of medical sciences, Tehran, Iran
- School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Meysam Abolmaali
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mojtahed
- School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Sevim Soleimani
- School of Medicine, Shahid Beheshti Medical University, Tehran, Iran
| | - Mahisa Mokhtari
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Jaber Hatam
- Department of Neurosurgery, Iran University of Medical Sciences, Tehran, Iran
| | | | | | - Mohammad Taghi Joghataei
- Cellular and Molecular Research Center, Iran university of medical sciences, Tehran, Iran
- School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Mirzaasgari
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Moghaddasi
- Department of Neurology, Iran University of Medical Sciences, Tehran, Iran
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354
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Prakash S, Srivastava R, Coulon PG, Dhanushkodi NR, Chentoufi AA, Tifrea DF, Edwards RA, Figueroa CJ, Schubl SD, Hsieh L, Buchmeier MJ, Bouziane M, Nesburn AB, Kuppermann BD, BenMohamed L. Genome-Wide B Cell, CD4 +, and CD8 + T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines. THE JOURNAL OF IMMUNOLOGY 2021; 206:2566-2582. [PMID: 33911008 DOI: 10.4049/jimmunol.2001438] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
Over the last two decades, there have been three deadly human outbreaks of coronaviruses (CoVs) caused by SARS-CoV, MERS-CoV, and SARS-CoV-2, which has caused the current COVID-19 global pandemic. All three deadly CoVs originated from bats and transmitted to humans via various intermediate animal reservoirs. It remains highly possible that other global COVID pandemics will emerge in the coming years caused by yet another spillover of a bat-derived SARS-like coronavirus (SL-CoV) into humans. Determining the Ag and the human B cells, CD4+ and CD8+ T cell epitope landscapes that are conserved among human and animal coronaviruses should inform in the development of future pan-coronavirus vaccines. In the current study, using several immunoinformatics and sequence alignment approaches, we identified several human B cell and CD4+ and CD8+ T cell epitopes that are highly conserved in 1) greater than 81,000 SARS-CoV-2 genome sequences identified in 190 countries on six continents; 2) six circulating CoVs that caused previous human outbreaks of the common cold; 3) nine SL-CoVs isolated from bats; 4) nine SL-CoV isolated from pangolins; 5) three SL-CoVs isolated from civet cats; and 6) four MERS strains isolated from camels. Furthermore, the identified epitopes: 1) recalled B cells and CD4+ and CD8+ T cells from both COVID-19 patients and healthy individuals who were never exposed to SARS-CoV-2, and 2) induced strong B cell and T cell responses in humanized HLA-DR1/HLA-A*02:01 double-transgenic mice. The findings pave the way to develop a preemptive multiepitope pan-coronavirus vaccine to protect against past, current, and future outbreaks.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Ruchi Srivastava
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Pierre-Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Aziz A Chentoufi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA
| | - Cesar J Figueroa
- Division of Trauma, Burns, Critical Care, and Acute Care Surgery, Department of Surgery, School of Medicine, University of California Irvine, Irvine, CA
| | - Sebastian D Schubl
- Division of Trauma, Burns, Critical Care, and Acute Care Surgery, Department of Surgery, School of Medicine, University of California Irvine, Irvine, CA
| | - Lanny Hsieh
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, University of California Irvine, Irvine, CA
| | - Michael J Buchmeier
- Center for Virus Research, Division of Infectious Disease, School of Medicine, University of California Irvine, Irvine, CA
| | | | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Irvine, CA; .,Center for Virus Research, Division of Infectious Disease, School of Medicine, University of California Irvine, Irvine, CA.,Institute for Immunology, School of Medicine, University of California Irvine, Irvine, CA
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355
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Schmidt KG, Nganou-Makamdop K, Tenbusch M, El Kenz B, Maier C, Lapuente D, Überla K, Spriewald B, Bergmann S, Harrer EG, Harrer T. SARS-CoV-2-Seronegative Subjects Target CTL Epitopes in the SARS-CoV-2 Nucleoprotein Cross-Reactive to Common Cold Coronaviruses. Front Immunol 2021; 12:627568. [PMID: 33995351 PMCID: PMC8113865 DOI: 10.3389/fimmu.2021.627568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
The beta-coronavirus SARS-CoV-2 induces severe disease (COVID-19) mainly in elderly persons with risk factors, whereas the majority of patients experience a mild course of infection. As the circulating common cold coronaviruses OC43 and HKU1 share some homologous sequences with SARS-CoV-2, beta-coronavirus cross-reactive T-cell responses could influence the susceptibility to SARS-CoV-2 infection and the course of COVID-19. To investigate the role of beta-coronavirus cross-reactive T-cells, we analyzed the T-cell response against a 15 amino acid long peptide (SCoV-DP15: DLSPRWYFYYLGTGP) from the SARS-CoV-2 nucleoprotein sequence with a high homology to the corresponding sequence (QLLPRWYFYYLGTGP) in OC43 and HKU1. SCoV-DP15-specific T-cells were detected in 4 out of 23 (17.4%) SARS-CoV-2-seronegative healthy donors. As HIV-1 infection is a potential risk factor for COVID-19, we also studied a cohort of HIV-1-infected patients on antiretroviral therapy. 44 out of these 116 HIV-1-infected patients (37.9%) showed a specific recognition of the SCoV-DP15 peptide or of shorter peptides within SCoV-DP15 by CD4+ T-cells and/or by CD8+ T-cells. We could define several new cross-reactive HLA-I-restricted epitopes in the SARS-CoV-2 nucleoprotein such as SPRWYFYYL (HLA-B*07, HLA-B*35), DLSPRWYFYY (HLA-A*02), LSPRWYFYY (HLA-A*29), WYFYYLGTGP and WYFYYLGT. Epitope specific CD8+ T-cell lines recognized corresponding epitopes within OC43 and HKU1 to a similar degree or even at lower peptide concentrations suggesting that they were induced by infection with OC43 or HKU1. Our results confirm that SARS-CoV-2-seronegative subjects can target SARS-CoV-2 not only by beta-coronavirus cross-reactive CD4+ T-cells but also by cross-reactive CD8+ cytotoxic T-cells (CTL). The delineation of cross-reactive T-cell epitopes contributes to an efficient epitope-specific immunomonitoring of SARS-CoV-2-specific T-cells. Further prospective studies are needed to prove a protective role of cross-reactive T-cells and their restricting HLA alleles for control of SARS-CoV-2 infection. The frequent observation of SARS-CoV-2-reactive T-cells in HIV-1-infected subjects could be a reason that treated HIV-1 infection does not seem to be a strong risk factor for the development of severe COVID-19.
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Affiliation(s)
- Katja G. Schmidt
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Krystelle Nganou-Makamdop
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Tenbusch
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Boutaina El Kenz
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Clara Maier
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Dennis Lapuente
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Spriewald
- Department of Medicine 5, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Silke Bergmann
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ellen G. Harrer
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Harrer
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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356
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Rammensee HG, Gouttefangeas C, Heidu S, Klein R, Preuß B, Walz JS, Nelde A, Haen SP, Reth M, Yang J, Tabatabai G, Bösmüller H, Hoffmann H, Schindler M, Planz O, Wiesmüller KH, Löffler MW. Designing a SARS-CoV-2 T-Cell-Inducing Vaccine for High-Risk Patient Groups. Vaccines (Basel) 2021; 9:428. [PMID: 33923363 PMCID: PMC8146137 DOI: 10.3390/vaccines9050428] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 01/21/2023] Open
Abstract
We describe the results of two vaccinations of a self-experimenting healthy volunteer with SARS-CoV-2-derived peptides performed in March and April 2020, respectively. The first set of peptides contained eight peptides predicted to bind to the individual's HLA molecules. The second set consisted of ten peptides predicted to bind promiscuously to several HLA-DR allotypes. The vaccine formulation contained the new TLR 1/2 agonist XS15 and was administered as an emulsion in Montanide as a single subcutaneous injection. Peripheral blood mononuclear cells isolated from blood drawn before and after vaccinations were assessed using Interferon-γ ELISpot assays and intracellular cytokine staining. We detected vaccine-induced CD4 T cell responses against six out of 11 peptides predicted to bind to HLA-DR after 19 days, following vaccination, for one peptide already at day 12. We used these results to support the design of a T-cell-inducing vaccine for application in high-risk patients, with weakened lymphocyte performance. Meanwhile, an according vaccine, incorporating T cell epitopes predominant in convalescents, is undergoing clinical trial testing.
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Affiliation(s)
- Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) “Controlling Microbes to Fight Infections”, University of Tübingen, 72076 Tübingen, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
| | - Sonja Heidu
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany; (R.K.); (B.P.)
| | - Beate Preuß
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany; (R.K.); (B.P.)
| | - Juliane Sarah Walz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK), Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Auerbachstr. 112, 70376 Stuttgart, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK), Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Sebastian P. Haen
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany;
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Michael Reth
- Signaling Research Centres BIOSS and CIBSS, Institute of Biology III, Department of Molecular Immunology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; (M.R.); (J.Y.)
| | - Jianying Yang
- Signaling Research Centres BIOSS and CIBSS, Institute of Biology III, Department of Molecular Immunology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany; (M.R.); (J.Y.)
| | - Ghazaleh Tabatabai
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany;
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, University Hospital Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Hans Bösmüller
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, 72076 Tübingen, Germany;
| | - Helen Hoffmann
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany;
| | - Oliver Planz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
| | | | - Markus W. Löffler
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany; (C.G.); (S.H.); (J.S.W.); (A.N.); (H.H.); (O.P.); (M.W.L.)
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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357
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Bilich T, Nelde A, Heitmann JS, Maringer Y, Roerden M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Rachfalski D, Märklin M, Stevanović S, Rammensee HG, Salih HR, Walz JS. T cell and antibody kinetics delineate SARS-CoV-2 peptides mediating long-term immune responses in COVID-19 convalescent individuals. Sci Transl Med 2021; 13:eabf7517. [PMID: 33723016 PMCID: PMC8128286 DOI: 10.1126/scitranslmed.abf7517] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/14/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Long-term immunological memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for the development of population-level immunity, which is the aim of vaccination approaches. Reports on rapidly decreasing antibody titers have led to questions regarding the efficacy of humoral immunity alone. The relevance of T cell memory after coronavirus disease 2019 (COVID-19) remains unclear. Here, we investigated SARS-CoV-2 antibody and T cell responses in matched samples of COVID-19 convalescent individuals up to 6 months after infection. Longitudinal analysis revealed decreasing and stable spike- and nucleocapsid-specific antibody responses, respectively. In contrast, functional T cell responses remained robust, and even increased, in both frequency and intensity. Single peptide mapping of T cell diversity over time identified open reading frame-independent, dominant T cell epitopes mediating long-term SARS-CoV-2 T cell responses. Identification of these epitopes may be fundamental for COVID-19 vaccine design.
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Affiliation(s)
- Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), 70376 Stuttgart, Germany
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358
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Müller TM, Becker E, Wiendl M, Schulze LL, Voskens C, Völkl S, Kremer AE, Neurath MF, Zundler S. Circulating Adaptive Immune Cells Expressing the Gut Homing Marker α4β7 Integrin Are Decreased in COVID-19. Front Immunol 2021; 12:639329. [PMID: 33959123 PMCID: PMC8093414 DOI: 10.3389/fimmu.2021.639329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background Infection with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a wide range of symptoms including gastrointestinal manifestations, and intestinal epithelial cells are a target of the virus. However, it is unknown how the intestinal immune system contributes to systemic immune responses in coronavirus disease 2019 (COVID-19). Methods We characterized peripheral blood lymphocytes from patients with active COVID-19 and convalescent patients as well as healthy controls by flow cytometry. Results The frequency and absolute number of circulating memory T and B cells expressing the gut homing integrin α4β7 integrin was reduced during COVID-19, whether gastrointestinal symptoms were present or not. While total IgA-expressing B cells were increased, gut-imprinted B cells with IgA expression were stable. Conclusion COVID-19 is associated with a decrease in circulating adaptive immune cells expressing the key gut homing marker α4β7 suggesting that these cells are preferentially recruited to extra-intestinal tissues independently of α4β7 or that the systemic immune response against SARS-CoV-2 is at least numerically dominated by extraintestinal, particularly pulmonary, immune cell priming.
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Affiliation(s)
- Tanja M Müller
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Emily Becker
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Maximilian Wiendl
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lisa Lou Schulze
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Caroline Voskens
- Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simon Völkl
- Department of Internal Medicine 5, Hematology and Clinical Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas E Kremer
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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359
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Saini SK, Hersby DS, Tamhane T, Povlsen HR, Amaya Hernandez SP, Nielsen M, Gang AO, Hadrup SR. SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8 + T cell activation in COVID-19 patients. Sci Immunol 2021; 6:eabf7550. [PMID: 33853928 PMCID: PMC8139428 DOI: 10.1126/sciimmunol.abf7550] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/08/2021] [Indexed: 12/11/2022]
Abstract
T cells are important for effective viral clearance, elimination of virus-infected cells and long-term disease protection. To examine the full-spectrum of CD8+ T cell immunity in COVID-19, we experimentally evaluated 3141 major histocompatibility (MHC) class I-binding peptides covering the complete SARS-CoV-2 genome. Using DNA-barcoded peptide-MHC complex (pMHC) multimers combined with a T cell phenotype panel, we report a comprehensive list of 122 immunogenic and a subset of immunodominant SARS-CoV-2 T cell epitopes. Substantial CD8+ T cell recognition was observed in COVID-19 patients, with up to 27% of all CD8+ lymphocytes interacting with SARS-CoV-2-derived epitopes. Most immunogenic regions were derived from open reading frame (ORF) 1 and ORF3, with ORF1 containing most of the immunodominant epitopes. CD8+ T cell recognition of lower affinity was also observed in healthy donors toward SARS-CoV-2-derived epitopes. This pre-existing T cell recognition signature was partially overlapping with the epitope landscape observed in COVID-19 patients and may drive the further expansion of T cell responses to SARS-CoV-2 infection. Importantly the phenotype of the SARS-CoV-2-specific CD8+ T cells, revealed a strong T cell activation in COVID-19 patients, while minimal T cell activation was seen in healthy individuals. We found that patients with severe disease displayed significantly larger SARS-CoV-2-specific T cell populations compared to patients with mild diseases and these T cells displayed a robust activation profile. These results further our understanding of T cell immunity to SARS-CoV-2 infection and hypothesize that strong antigen-specific T cell responses are associated with different disease outcomes.
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Affiliation(s)
- Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Ditte Stampe Hersby
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helle Rus Povlsen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susana Patricia Amaya Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne Ortved Gang
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
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360
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Ziemssen F, Feng YS, Schnichels S, Bayyoud T, Ueffing M, Bartz-Schmidt KU, Martus P, Peter A. Testing for SARS-CoV-2 seroprevalence: experiences of a tertiary eye centre. BMJ Open Ophthalmol 2021; 6:e000688. [PMID: 34192154 PMCID: PMC8050881 DOI: 10.1136/bmjophth-2020-000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 03/13/2021] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The actual prevalence of a SARS-CoV-2 infection and the individual assessment of being or having been infected may differ. Facing the great uncertainty-especially at the beginning of the pandemic-and the possibility of asymptomatic or mildly symptomatic, subclinical infections, we evaluate the experience of SARS-CoV-2 antibody screening at a tertiary clinical setting. METHODS AND ANALYSIS All employees of a tertiary eye centre and a research institute of ophthalmology were offered antibody testing in May 2020, using a sequential combination of different validated assays/antigens and point-of-care (POC) testing for a subset (NCT04446338). Before taking blood, a systematic inquiry into past symptoms, known contacts and a subjective self-assessment was documented. The correlations between serostatus, patient contacts and demographic characteristics were analysed. Different tests were compared by Kappa statistics. RESULTS Among 318 participants, SARS-CoV-2 antibodies were detected in 9 employees. Chemiluminescence assays (chemiluminescence immunoassay and electrochemiluminescence) showed superior specificity and high reproducibility, compared with ELISA and POC results.In contrast to the low seropositivity (2.8%) of healthcare workers, higher than that of the other departments of the hospital, a large proportion mistakenly assumed that they might have already been infected. Antiviral antibody titres increased and remained on a plateau for at least 3 months. CONCLUSIONS The great demand and acceptance confirmed the benefit of highly sensitive testing methods in the early phase of the pandemic. The coincidence of low seroprevalence and anxious employees may have contributed to internalising the need of hygiene measures.
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Affiliation(s)
- Focke Ziemssen
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - You-Shan Feng
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Sven Schnichels
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Tarek Bayyoud
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | | | - Peter Martus
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls Universitat Tubingen, Tubingen, Germany
| | - Andreas Peter
- Institute of Clinical Chemistry and Pathobichemistry, Department of Internal Medicine, Eberhard Karls Universitat Tubingen, Tubingen, Germany
- Institute for Diabetes Research and Metabolic Diseases, German Center for Diabetes Research (DZD) Helmholtz Zentrum München at the University of Tübingen, Eberhard Karls Universitat Tubingen, Tubingen, Germany
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361
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Sohail MS, Ahmed SF, Quadeer AA, McKay MR. In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives. Adv Drug Deliv Rev 2021; 171:29-47. [PMID: 33465451 PMCID: PMC7832442 DOI: 10.1016/j.addr.2021.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/31/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Growing evidence suggests that T cells may play a critical role in combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, COVID-19 vaccines that can elicit a robust T cell response may be particularly important. The design, development and experimental evaluation of such vaccines is aided by an understanding of the landscape of T cell epitopes of SARS-CoV-2, which is largely unknown. Due to the challenges of identifying epitopes experimentally, many studies have proposed the use of in silico methods. Here, we present a review of the in silico methods that have been used for the prediction of SARS-CoV-2 T cell epitopes. These methods employ a diverse set of technical approaches, often rooted in machine learning. A performance comparison is provided based on the ability to identify a specific set of immunogenic epitopes that have been determined experimentally to be targeted by T cells in convalescent COVID-19 patients, shedding light on the relative performance merits of the different approaches adopted by the in silico studies. The review also puts forward perspectives for future research directions.
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Affiliation(s)
- Muhammad Saqib Sohail
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Syed Faraz Ahmed
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
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362
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Schöllhorn A, Schuhmacher J, Besedovsky L, Fendel R, Jensen ATR, Stevanović S, Lange T, Rammensee HG, Born J, Gouttefangeas C, Dimitrov S. Integrin Activation Enables Sensitive Detection of Functional CD4 + and CD8 + T Cells: Application to Characterize SARS-CoV-2 Immunity. Front Immunol 2021; 12:626308. [PMID: 33854501 PMCID: PMC8040333 DOI: 10.3389/fimmu.2021.626308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 01/28/2023] Open
Abstract
We have previously shown that conformational change in the β2-integrin is a very early activation marker that can be detected with fluorescent multimers of its ligand intercellular adhesion molecule (ICAM)-1 for rapid assessment of antigen-specific CD8+ T cells. In this study, we describe a modified protocol of this assay for sensitive detection of functional antigen-specific CD4+ T cells using a monoclonal antibody (clone m24 Ab) specific for the open, high-affinity conformation of the β2-integrin. The kinetics of β2-integrin activation was different on CD4+ and CD8+ T cells (several hours vs. few minutes, respectively); however, m24 Ab readily stained both cell types 4–6 h after antigen stimulation. With this protocol, we were able to monitor ex vivo effector and memory CD4+ and CD8+ T cells specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cytomegalovirus (CMV), Epstein–Barr virus (EBV), and hepatitis B virus (HBV) in whole blood or cryopreserved peripheral blood mononuclear cells (PBMCs) of infected or vaccinated individuals. By costaining β2-integrin with m24 and CD154 Abs, we assessed extremely low frequencies of polyfunctional CD4+ T cell responses. The novel assay used in this study allows very sensitive and simultaneous screening of both CD4+ and CD8+ T cell reactivities, with versatile applicability in clinical and vaccination studies.
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Affiliation(s)
- Anna Schöllhorn
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Juliane Schuhmacher
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Luciana Besedovsky
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Anja T R Jensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies, " University of Tübingen, Tübingen, Germany
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies, " University of Tübingen, Tübingen, Germany
| | - Jan Born
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tübingen (IDM), Tübingen, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies, " University of Tübingen, Tübingen, Germany
| | - Stoyan Dimitrov
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany
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363
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Tan H, Lee WS, Wragg KM, Nelson C, Esterbauer R, Kelly HG, Amarasena T, Jones R, Starkey G, Wang BZ, Yoshino O, Tiang T, Grayson ML, Opdam H, D'Costa R, Vago A, Mackay LK, Gordon CL, Wheatley AK, Kent SJ, Juno JA. Adaptive immunity to human coronaviruses is widespread but low in magnitude. Clin Transl Immunology 2021; 10:e1264. [PMID: 33747512 PMCID: PMC7968850 DOI: 10.1002/cti2.1264] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Endemic human coronaviruses (hCoVs) circulate worldwide but cause minimal mortality. Although seroconversion to hCoV is near ubiquitous during childhood, little is known about hCoV-specific T-cell memory in adults. METHODS We quantified CD4 T-cell and antibody responses to hCoV spike antigens in 42 SARS-CoV-2-uninfected individuals. Antigen-specific memory T cells and circulating T follicular helper (cTFH) cells were identified using an activation-induced marker assay and characterised for memory phenotype and chemokine receptor expression. RESULTS T-cell responses were widespread within conventional memory and cTFH compartments but did not correlate with IgG titres. SARS-CoV-2 cross-reactive T cells were observed in 48% of participants and correlated with HKU1 memory. hCoV-specific T cells exhibited a CCR6+ central memory phenotype in the blood, but were enriched for frequency and CXCR3 expression in human lung-draining lymph nodes. CONCLUSION Overall, hCoV-specific humoral and cellular memory are independently maintained, with a shared phenotype existing among coronavirus-specific CD4 T cells. This understanding of endemic coronavirus immunity provides insight into the homeostatic maintenance of immune responses that are likely to be critical components of protection against SARS-CoV-2.
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Affiliation(s)
- Hyon‐Xhi Tan
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Wen Shi Lee
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Kathleen M Wragg
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Christina Nelson
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Robyn Esterbauer
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Hannah G Kelly
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
- Australian Research Council Centre for Excellence in Convergent Bio‐Nano Science and TechnologyUniversity of MelbourneMelbourneVICAustralia
| | - Thakshila Amarasena
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Robert Jones
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | - Graham Starkey
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | - Bao Zhong Wang
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | - Osamu Yoshino
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | - Thomas Tiang
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | | | - Helen Opdam
- DonateLifeThe Australian Organ and Tissue AuthorityCarltonVICAustralia
- Department of Intensive CareAustin HealthHeidelbergVICAustralia
| | - Rohit D'Costa
- DonateLife VictoriaCarltonVICAustralia
- Intensive Care UnitThe Royal Melbourne HospitalParkvilleVICAustralia
| | - Angela Vago
- Department of SurgeryAustin HealthHeidelbergVICAustralia
| | - Laura K Mackay
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Claire L Gordon
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
- Department of Infectious DiseasesAustin HealthHeidelbergVICAustralia
| | - Adam K Wheatley
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
| | - Stephen J Kent
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
- Australian Research Council Centre for Excellence in Convergent Bio‐Nano Science and TechnologyUniversity of MelbourneMelbourneVICAustralia
- Melbourne Sexual Health Centre and Department of Infectious DiseasesAlfred Hospital and Central Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Jennifer A Juno
- Department of Microbiology and ImmunologyUniversity of Melbourne, at the Peter Doherty institute for Infection and ImmunityMelbourneVICAustralia
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364
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Agerer B, Koblischke M, Gudipati V, Montaño-Gutierrez LF, Smyth M, Popa A, Genger JW, Endler L, Florian DM, Mühlgrabner V, Graninger M, Aberle SW, Husa AM, Shaw LE, Lercher A, Gattinger P, Torralba-Gombau R, Trapin D, Penz T, Barreca D, Fae I, Wenda S, Traugott M, Walder G, Pickl WF, Thiel V, Allerberger F, Stockinger H, Puchhammer-Stöckl E, Weninger W, Fischer G, Hoepler W, Pawelka E, Zoufaly A, Valenta R, Bock C, Paster W, Geyeregger R, Farlik M, Halbritter F, Huppa JB, Aberle JH, Bergthaler A. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses. Sci Immunol 2021; 6:6/57/eabg6461. [PMID: 33664060 PMCID: PMC8224398 DOI: 10.1126/sciimmunol.abg6461] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/27/2021] [Indexed: 12/26/2022]
Abstract
CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8+ T cells isolated from HLA-matched COVID-19 patients. Single cell RNA sequencing of ex vivo expanded, tetramer-sorted CD8+ T cells from COVID-19 patients further revealed qualitative differences in the transcriptional response to mutant peptides. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through point mutations in MHC-I-restricted viral epitopes.
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Affiliation(s)
- Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Venugopal Gudipati
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - David M Florian
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Vanessa Mühlgrabner
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Anna-Maria Husa
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa Ellen Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pia Gattinger
- Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria
| | - Ricard Torralba-Gombau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Doris Trapin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ingrid Fae
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Gernot Walder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Winfried F Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gottfried Fischer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Erich Pawelka
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Alexander Zoufaly
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria.,Laboratory for Immunopathology, Department of Clinical Immunology and Allergy, First Moscow State Medical University Sechenov, Moscow, Russia.,NRC Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Paster
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - René Geyeregger
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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365
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Dijkstra JM, Frenette AP, Dixon B. Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses. F1000Res 2021; 10:196. [PMID: 34026045 PMCID: PMC8108557 DOI: 10.12688/f1000research.51479.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In the spring of 2020, we and others hypothesized that T cells in COVID-19 patients may recognize identical protein fragments shared between the coronaviruses of the common cold and COVID-19 and thereby confer cross-virus immune memory. Here, we look at this issue by screening studies that, since that time, have experimentally addressed COVID-19 associated T cell specificities. Currently, the identical T cell epitope shared between COVID-19 and common cold coronaviruses most convincingly identified as immunogenic is the CD8 + T cell epitope VYIGDPAQL if presented by the MHC class I allele HLA-A*24:02. The HLA-A*24:02 allele is found in the majority of Japanese individuals and several indigenous populations in Asia, Oceania, and the Americas. In combination with histories of common cold infections, HLA-A*24:02 may affect their protection from COVID-19.
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Affiliation(s)
- Johannes M. Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health Universit, Toyoake-shi, 470-1192, Japan
| | - Aaron P. Frenette
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
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366
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De Giorgi V, West KA, Henning AN, Chen L, Holbrook MR, Gross R, Liang J, Postnikova E, Trenbeath J, Pogue S, Scinto T, Alter HJ, Cantilena CC. Anti-SARS-CoV-2 Serology persistence over time in COVID-19 Convalescent Plasma Donors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33758897 DOI: 10.1101/2021.03.08.21253093] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Characterizing the kinetics of the antibody response to SARS□CoV□2 is of critical importance to developing strategies that may mitigate the public health burden of COVID-19. We sought to determine how circulating antibody levels change over time following natural infection. Methods/Materials We conducted a prospective, longitudinal analysis of COVID-19 convalescent plasma (CCP) donors at multiple time points over a 9-month period. At each study visit, subjects either donated plasma or only had study samples drawn. In all cases, anti-SARS-CoV-2 donor testing was performed using semi-quantitative chemiluminescent immunoassays (ChLIA) targeting subunit 1 (S1) of the SARS-CoV-2 spike (S) protein, and an in-house fluorescence reduction neutralization assay (FRNA). Results From April to November 2020 we enrolled 202 donors, mean age 47.3 ±14.7 years, 55% female, 75% Caucasian. Most donors reported a mild clinical course (91%, n=171) without hospitalization. One hundred and five (105) (52%) donors presented for repeat visits with a median 42 (12-163) days between visits. The final visit occurred at a median 160 (53-273) days post-symptom resolution. Total anti-SARS-CoV-2 antibodies (Ab), SARS-CoV-2 specific IgG and neutralizing antibodies were detected in 97.5%, 91.1%, and 74% of donors respectively at initial presentation. Neutralizing Ab titers based on FRNA 50 were positively associated with mean IgG levels (p = <0.0001). Mean IgG levels and neutralizing titers were positively associated with COVID-19 severity, increased donor age and BMI (p=0.0006 and p=0.0028, p=0.0083 and p=0.0363, (p=0.0008 and p=0.0018, respectively). Over the course of repeat visits, IgG decreased in 74.1% of donors; FRNA 50 decreased in 44.4% and remained unchanged in 33.3% of repeat donors. A weak negative correlation was observed between total Ab levels and number of days post-symptom recovery (r = 0.09). Conclusion Anti-SARS-CoV-2 antibodies were identified in 97% of convalescent donors at initial presentation. In a cohort that largely did not require hospitalization. IgG and neutralizing antibodies were positively correlated with age, BMI and clinical severity, and persisted for up to 9 months post-recovery from natural infection. On repeat presentation, IgG anti-SARS-CoV-2 levels decreased in 56% of repeat donors. Overall, these data suggest that CP donors possess a wide range of IgG and neutralizing antibody levels that are proportionally distributed across demographics, with the exception of age, BMI and clinical severity.
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367
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Gao L, Zhou J, Yang S, Wang L, Chen X, Yang Y, Li R, Pan Z, Zhao J, Li Z, Huang Q, Tang J, Hu L, Liu P, Zhang G, Chen Y, Ye L. The dichotomous and incomplete adaptive immunity in COVID-19 patients with different disease severity. Signal Transduct Target Ther 2021; 6:113. [PMID: 33686064 PMCID: PMC7938043 DOI: 10.1038/s41392-021-00525-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 12/28/2022] Open
Abstract
The adaptive immunity that protects patients from coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not well characterized. In particular, the asymptomatic patients have been found to induce weak and transient SARS-CoV-2 antibody responses, but the underlying mechanisms remain unknown; meanwhile, the protective immunity that guide the recovery of these asymptomatic patients is elusive. Here, we characterized SARS-CoV-2-specific B-cell and T-cell responses in 10 asymptomatic patients and 64 patients with other disease severity (mild, n = 10, moderate, n = 32, severe, n = 12) and found that asymptomatic or mild symptomatic patients failed to mount virus-specific germinal center (GC) B cell responses that result in robust and prolonged humoral immunity, assessed by GC response indicators including follicular helper T (TFH) cell and memory B cell responses as well as serum CXCL13 levels. Alternatively, these patients mounted potent virus-specific TH1 and CD8+ T cell responses. In sharp contrast, patients of moderate or severe disease induced vigorous virus-specific GC B cell responses and associated TFH responses; however, the virus-specific TH1 and CD8+ T cells were minimally induced in these patients. These results, therefore, uncovered the protective immunity in asymptomatic patients and also revealed the strikingly dichotomous and incomplete humoral and cellular immune responses in COVID-19 patients with different disease severity, providing important insights into rational design of effective COVID-19 vaccines.
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Affiliation(s)
- Leiqiong Gao
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jing Zhou
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Sen Yang
- Chongqing Public Health Medical Center, Chongqing, China
| | - Lisha Wang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Xiangyu Chen
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yang Yang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Ren Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiwei Pan
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhirong Li
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qizhao Huang
- Cancer Center, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Li Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Pinghuang Liu
- Comparative Immunology Research Center, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Yaokai Chen
- Chongqing Public Health Medical Center, Chongqing, China.
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, China.
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368
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Casado JL, Häemmerle J, Vizcarra P, Velasco H, Velasco T, Fernandez-Escribano M, Vallejo A. SARS CoV-2 infections in healthcare workers with a pre-existing T-cell response: a prospective cohort study. Clin Microbiol Infect 2021; 27:916.e1-916.e4. [PMID: 33667629 PMCID: PMC7923873 DOI: 10.1016/j.cmi.2021.02.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/20/2022]
Abstract
Objective T-cell responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are observed in unexposed individuals. We evaluated the impact of this pre-existing cellular response on incident SARS-CoV-2 infections. Methods This was a follow-up study of 38 seronegative healthcare workers (HCWs) with previous evaluation of CD8+ and CD4+ T-cell responses after stimulation with SARS-CoV-2 structural proteins. Infection was considered in the presence of a positive RT-PCR test and/or confirmed seroconversion. Results Twenty of the 38 HCWs included (53%) had a previous specific CD8+ T-cell response to peptides encompassing the spike protein (S) in 13 (34%), the membrane (M) in 17 (45%), or/and the nucleocapsid (N) in three (8%). During a follow-up of 189 days (interquartile range (IQR) 172–195), 11 HCWs (29%) had an RT-PCR-positive test (n = 9) or seroconverted (n = 2). Median duration of symptoms was 2 days (IQR 0–7), and time to negative RT-PCR was 9 days (IQR 4–10). Notably, six incident infections (55%) occurred in HCWs with a pre-existing T-cell response (30% of those with a cellular response), who showed a significantly lower duration of symptoms (three were asymptomatic). Three of the six HCWs having a previous T-cell response continued to test seronegative. All the infected patients developed a robust T-cell response to different structural SARS-CoV-2 proteins, especially to protein S (91%). Conclusion A pre-existing T-cell response does not seem to reduce incident SARS-CoV-2 infections, but it may contribute to asymptomatic or mild disease, rapid viral clearance and differences in seroconversion.
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Affiliation(s)
- José L Casado
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain.
| | - Johannes Häemmerle
- Department of Prevention of Occupational Risks, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Hector Velasco
- Laboratory of Immunovirology, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Tamara Velasco
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | | | - Alejandro Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Madrid, Spain; Laboratory of Immunovirology, Hospital Universitario Ramon y Cajal, Madrid, Spain
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369
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Pollet J, Chen WH, Strych U. Recombinant protein vaccines, a proven approach against coronavirus pandemics. Adv Drug Deliv Rev 2021; 170:71-82. [PMID: 33421475 PMCID: PMC7788321 DOI: 10.1016/j.addr.2021.01.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023]
Abstract
With the COVID-19 pandemic now ongoing for close to a year, people all over the world are still waiting for a vaccine to become available. The initial focus of accelerated global research and development efforts to bring a vaccine to market as soon as possible was on novel platform technologies that promised speed but had limited history in the clinic. In contrast, recombinant protein vaccines, with numerous examples in the clinic for many years, missed out on the early wave of investments from government and industry. Emerging data are now surfacing suggesting that recombinant protein vaccines indeed might offer an advantage or complement to the nucleic acid or viral vector vaccines that will likely reach the clinic faster. Here, we summarize the current public information on the nature and on the development status of recombinant subunit antigens and adjuvants targeting SARS-CoV-2 infections.
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Affiliation(s)
- Jeroen Pollet
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital Center for Vaccine Development, Baylor College of Medicine, 1102 Bates Street, Houston, TX, United States of America.
| | - Wen-Hsiang Chen
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital Center for Vaccine Development, Baylor College of Medicine, 1102 Bates Street, Houston, TX, United States of America
| | - Ulrich Strych
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital Center for Vaccine Development, Baylor College of Medicine, 1102 Bates Street, Houston, TX, United States of America
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370
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Tarke A, Sidney J, Methot N, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, da Silva Antunes R, Frazier A, Rawlings SA, Smith DM, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. Negligible impact of SARS-CoV-2 variants on CD4 + and CD8 + T cell reactivity in COVID-19 exposed donors and vaccinees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.27.433180. [PMID: 33688655 PMCID: PMC7941626 DOI: 10.1101/2021.02.27.433180] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of SARS-CoV-2 variants highlighted the need to better understand adaptive immune responses to this virus. It is important to address whether also CD4+ and CD8+ T cell responses are affected, because of the role they play in disease resolution and modulation of COVID-19 disease severity. Here we performed a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. Similarly, we demonstrate that the sequences of the vast majority of SARS-CoV-2 T cell epitopes are not affected by the mutations found in the variants analyzed. Overall, the results demonstrate that CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations found in the SARS-CoV-2 variants.
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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 Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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
| | - Yun Zhang
- J. Craig Venter Institute, 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
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Bjoern Peters
- 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
| | - Richard H Scheuermann
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California, San Diego, CA 92093
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Shane Crotty
- 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
| | - 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
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371
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High-throughput approaches of diagnosis and therapies for COVID-19: antibody panels, proteomics and metabolomics. FUTURE DRUG DISCOVERY 2021. [PMCID: PMC7714045 DOI: 10.4155/fdd-2020-0027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The urgent need for diagnostics and therapeutics against the COVID-19 pandemic has shown the great potential of antibodies, proteomics and metabolomics in this direction. Several clinical trials are underway using antibodies from COVID-19 patients that show very specific and strong binding to viral proteins leading to neutralization. On the other hand, proteomic and metabolomic profiles of COVID-19 patients present novel diagnostic biomarkers to predict patient outcomes and enable the development of personalized therapeutics to target the dysregulated pathways, as revealed by those profiles. Here, we discuss how studies based on antibodies, proteomics and metabolomics contribute to the development of diagnostics and therapeutics against COVID-19. The elegant technology can extend to high-throughput, rapid and reliable drug discovery strategies of the future. In order to prevent and treat the ongoing COVID-19 pandemic, several groups around the world are focused on a detailed understanding of the biology of SARS-CoV-2 infection, the biological events occurring inside the patients and the response of the patients to the infection. SARS-CoV-2 is the coronavirus that causes COVID-19. Some of the approaches to combat the pandemic have provided important results that can help toward therapeutic developments against COVID-19. This review discusses three such areas – antibody treatment to prevent COVID-19 infection, analysis of changes in protein profiles of COVID-19 patients, and analysis of metabolism or energy-related changes in COVID-19 patients. Antibodies are molecules produced in the host’s body as a defense response to infection. Antibodies extracted from patients who recovered from COVID-19 have been used to successfully manufacture large amounts of antibodies to treat COVID-19 patients. The analysis of protein and metabolism profiles of COVID-19 patients has shown that several proteins and metabolism-related entities in the body are either upregulated or downregulated in COVID-19. These abnormal levels can either be attenuated by medical intervention or can be monitored as indicators of COVID-19 diagnosis. Overall, antibodies, protein and metabolism profiles are three important tools, among several others, that are helpful in combating the COVID-19 pandemic.
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372
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Exploring beyond clinical routine SARS-CoV-2 serology using MultiCoV-Ab to evaluate endemic coronavirus cross-reactivity. Nat Commun 2021; 12:1152. [PMID: 33608538 PMCID: PMC7896075 DOI: 10.1038/s41467-021-20973-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
The humoral immune response to SARS-CoV-2 is a benchmark for immunity and detailed analysis is required to understand the manifestation and progression of COVID-19, monitor seroconversion within the general population, and support vaccine development. The majority of currently available commercial serological assays only quantify the SARS-CoV-2 antibody response against individual antigens, limiting our understanding of the immune response. To overcome this, we have developed a multiplex immunoassay (MultiCoV-Ab) including spike and nucleocapsid proteins of SARS-CoV-2 and the endemic human coronaviruses. Compared to three broadly used commercial in vitro diagnostic tests, our MultiCoV-Ab achieves a higher sensitivity and specificity when analyzing a well-characterized sample set of SARS-CoV-2 infected and uninfected individuals. We find a high response against endemic coronaviruses in our sample set, but no consistent cross-reactive IgG response patterns against SARS-CoV-2. Here we show a robust, high-content-enabled, antigen-saving multiplex assay suited to both monitoring vaccination studies and facilitating epidemiologic screenings for humoral immunity towards pandemic and endemic coronaviruses.
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373
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Sette A, Crotty S. Adaptive immunity to SARS-CoV-2 and COVID-19. Cell 2021; 184:861-880. [PMID: 33497610 PMCID: PMC7803150 DOI: 10.1016/j.cell.2021.01.007] [Citation(s) in RCA: 1146] [Impact Index Per Article: 382.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 12/19/2022]
Abstract
The adaptive immune system is important for control of most viral infections. The three fundamental components of the adaptive immune system are B cells (the source of antibodies), CD4+ T cells, and CD8+ T cells. The armamentarium of B cells, CD4+ T cells, and CD8+ T cells has differing roles in different viral infections and in vaccines, and thus it is critical to directly study adaptive immunity to SARS-CoV-2 to understand COVID-19. Knowledge is now available on relationships between antigen-specific immune responses and SARS-CoV-2 infection. Although more studies are needed, a picture has begun to emerge that reveals that CD4+ T cells, CD8+ T cells, and neutralizing antibodies all contribute to control of SARS-CoV-2 in both non-hospitalized and hospitalized cases of COVID-19. The specific functions and kinetics of these adaptive immune responses are discussed, as well as their interplay with innate immunity and implications for COVID-19 vaccines and immune memory against re-infection.
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Affiliation(s)
- 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
| | - Shane Crotty
- 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.
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374
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Rha MS, Kim AR, Shin EC. SARS-CoV-2-Specific T Cell Responses in Patients with COVID-19 and Unexposed Individuals. Immune Netw 2021; 21:e2. [PMID: 33728095 PMCID: PMC7937509 DOI: 10.4110/in.2021.21.e2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes coronavirus disease 2019 (COVID-19), an ongoing pandemic disease. In the current review, we describe SARS-CoV-2-specific CD4+ and CD8+ T-cell responses in acute and convalescent COVID-19 patients. We also discuss the relationships between COVID-19 severity and SARS-CoV-2-specific T-cell responses and summarize recent reports regarding SARS-CoV-2-reactive T cells in SARS-CoV-2-unexposed individuals. These T cells may be cross-reactive cells primed by previous infection with human common-cold coronaviruses. Finally, we outline SARS-CoV-2-specific T-cell responses in the context of vaccination. A better understanding of SARS-CoV-2-specific T-cell responses is needed to develop effective vaccines and therapeutics.
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Affiliation(s)
- Min-Seok Rha
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - A Reum Kim
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Eui-Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,The Center for Epidemic Preparedness, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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375
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Identification of HLA-A*02:01-restricted candidate epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2 that may be natural targets of CD8 + T cell recognition in vivo. J Virol 2021; 95:JVI.01837-20. [PMID: 33268522 PMCID: PMC8092843 DOI: 10.1128/jvi.01837-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
COVID-19 vaccines are being rapidly developed and human trials are underway. Almost all of these vaccines have been designed to induce antibodies targeting spike protein of SARS-CoV-2 in expectation of neutralizing activities. However, non-neutralizing antibodies are at risk of causing antibody-dependent enhancement. Further, the longevity of SARS-CoV-2-specific antibodies is very short. Therefore, in addition to antibody-induced vaccines, novel vaccines on the basis of SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs) should be considered in the vaccine development. Here, we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Eighty-two peptides were firstly predicted as epitope candidates on bioinformatics. Fifty-four in 82 peptides showed high or medium binding affinities to HLA-A*02:01. HLA-A*02:01 transgenic mice were then immunized with each of the 54 peptides encapsulated into liposomes. The intracellular cytokine staining assay revealed that 18 out of 54 peptides were CTL epitopes because of the induction of IFN-γ-producing CD8+ T cells. In the 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant CTL epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant over the other peptides. Surprisingly, all mice immunized with the liposomal 10 peptide mixture did not show the same reaction pattern to the 10 peptides. There were three response patterns, suggesting the existence of an immunodominance hierarchy following peptide vaccination, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.IMPORTANCE For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three reaction patterns, suggesting the existence of an immunodominance hierarchy following peptide vaccination, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.
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376
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Persistence of SARS-CoV-2-specific B and T cell responses in convalescent COVID-19 patients 6-8 months after the infection. MED 2021; 2:281-295.e4. [PMID: 33589885 PMCID: PMC7874960 DOI: 10.1016/j.medj.2021.02.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/28/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
Background Monitoring the adaptive immune responses during the natural course of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection provides useful information for the development of vaccination strategies against this virus and its emerging variants. We thus profiled the serum anti-SARS-CoV-2 antibody (Ab) levels and specific memory B and T cell responses in convalescent coronavirus disease 2019 (COVID-19) patients. Methods A total of 119 samples from 88 convalescent donors who experienced mild to critical disease were tested for the presence of elevated anti-spike and anti-receptor binding domain Ab levels over a period of 8 months. In addition, the levels of SARS-CoV-2 neutralizing Abs and specific memory B and T cell responses were tested in a subset of samples. Findings Anti-SARS-CoV-2 Abs were present in 85% of the samples collected within 4 weeks after the onset of symptoms in COVID-19 patients. Levels of specific immunoglobulin M (IgM)/IgA Abs declined after 1 month, while levels of specific IgG Abs and plasma neutralizing activities remained relatively stable up to 6 months after diagnosis. Anti-SARS-CoV-2 IgG Abs were still present, although at a significantly lower level, in 80% of the samples collected at 6-8 months after symptom onset. SARS-CoV-2-specific memory B and T cell responses developed with time and were persistent in all of the patients followed up for 6-8 months. Conclusions Our data suggest that protective adaptive immunity following natural infection of SARS-CoV-2 may persist for at least 6-8 months, regardless of disease severity. Development of medium- or long-term protective immunity through vaccination may thus be possible. Funding This project was supported by the European Union's Horizon 2020 research and innovation programme (ATAC, no. 101003650), the Italian Ministry of Health (Ricerca Finalizzata grant no. GR-2013-02358399), the Center for Innovative Medicine, and the Swedish Research Council. J.A. was supported by the SciLifeLab/KAW national COVID-19 research program project grant 2020.
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377
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Musanabaganwa C, Cubaka V, Mpabuka E, Semakula M, Nahayo E, Hedt-Gauthier BL, Ng KCS, Murray MB, Kateera F, Mutesa L, Nsanzimana S. One hundred thirty-three observed COVID-19 deaths in 10 months: unpacking lower than predicted mortality in Rwanda. BMJ Glob Health 2021; 6:e004547. [PMID: 33627363 PMCID: PMC7907833 DOI: 10.1136/bmjgh-2020-004547] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
The African region was predicted to have worse COVID-19 infection and death rates due to challenging health systems and social determinants of health. However, in the 10 months after its first case, Rwanda recorded 10316 cases and 133 COVID-19-related deaths translating to a case fatality rate (CFR) of 1.3%, which raised the question: why does Rwanda have a low COVID-19 CFR? Here we analysed COVID-19 data and explored possible explanations to better understand the disease burden in the context of Rwanda's infection control strategies.We investigated whether the age distribution plays a role in the observed low CFR in Rwanda by comparing the expected number of deaths for 10-year age bands based on the CFR reported in other countries with the observed number of deaths for each age group. We found that the age-specific CFRs in Rwanda are similar to or, in some older age groups, slightly higher than those in other countries, suggesting that the lower population level CFR reflects the younger age structure in Rwanda, rather than a lower risk of death conditional on age. We also accounted for Rwanda's comprehensive SARS-CoV-2 testing strategies and reliable documentation of COVID-19-related deaths and deduced that these measures may have allowed them to likely identify more asymptomatic or mild cases than other countries and reduced their reported CFR.Overall, the observed low COVID-19 deaths in Rwanda is likely influenced by the combination of effective infection control strategies, reliable identification of cases and reporting of deaths, and the population's young age structure.
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Affiliation(s)
| | - Vincent Cubaka
- Department of Research and Training, Partners in Health Rwanda, Kigali, Rwanda
| | - Etienne Mpabuka
- Medical Research Center, Rwanda Biomedical Center, Kigali, Rwanda
| | | | - Ernest Nahayo
- Rwanda Military Hospital, Kigali, Kigali City, Rwanda
| | - Bethany L Hedt-Gauthier
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Kamela C S Ng
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Fredrick Kateera
- Department of Research and Training, Partners in Health Rwanda, Kigali, Rwanda
| | - Leon Mutesa
- Center of Human Genetics, University of Rwanda College of Medicine and Health Sciences, Kigali, Rwanda
| | - Sabin Nsanzimana
- Medical Research Center, Rwanda Biomedical Center, Kigali, Rwanda
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378
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Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. CELL REPORTS MEDICINE 2021; 2:100204. [PMID: 33521695 PMCID: PMC7837622 DOI: 10.1016/j.xcrm.2021.100204] [Citation(s) in RCA: 322] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens and precisely measure virus-specific CD4+ and CD8+ T cells, we study epitope-specific T cell responses of 99 convalescent coronavirus disease 2019 (COVID-19) cases. The SARS-CoV-2 proteome is probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of human leukocyte antigen (HLA) alleles for class II responses. For HLA class I, we study an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identify several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance are observed, which differ for CD4+ T cells, CD8+ T cells, and antibodies. The class I and class II epitopes are combined into epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+ and CD8+ T cells.
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379
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Shrotri M, van Schalkwyk MCI, Post N, Eddy D, Huntley C, Leeman D, Rigby S, Williams SV, Bermingham WH, Kellam P, Maher J, Shields AM, Amirthalingam G, Peacock SJ, Ismail SA. T cell response to SARS-CoV-2 infection in humans: A systematic review. PLoS One 2021; 16:e0245532. [PMID: 33493185 PMCID: PMC7833159 DOI: 10.1371/journal.pone.0245532] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Understanding the T cell response to SARS-CoV-2 is critical to vaccine development, epidemiological surveillance and disease control strategies. This systematic review critically evaluates and synthesises the relevant peer-reviewed and pre-print literature published from 01/01/2020-26/06/2020. METHODS For this systematic review, keyword-structured literature searches were carried out in MEDLINE, Embase and COVID-19 Primer. Papers were independently screened by two researchers, with arbitration of disagreements by a third researcher. Data were independently extracted into a pre-designed Excel template and studies critically appraised using a modified version of the MetaQAT tool, with resolution of disagreements by consensus. Findings were narratively synthesised. RESULTS 61 articles were included. 55 (90%) studies used observational designs, 50 (82%) involved hospitalised patients with higher acuity illness, and the majority had important limitations. Symptomatic adult COVID-19 cases consistently show peripheral T cell lymphopenia, which positively correlates with increased disease severity, duration of RNA positivity, and non-survival; while asymptomatic and paediatric cases display preserved counts. People with severe or critical disease generally develop more robust, virus-specific T cell responses. T cell memory and effector function has been demonstrated against multiple viral epitopes, and, cross-reactive T cell responses have been demonstrated in unexposed and uninfected adults, but the significance for protection and susceptibility, respectively, remains unclear. CONCLUSION A complex pattern of T cell response to SARS-CoV-2 infection has been demonstrated, but inferences regarding population level immunity are hampered by significant methodological limitations and heterogeneity between studies, as well as a striking lack of research in asymptomatic or pauci-symptomatic individuals. In contrast to antibody responses, population-level surveillance of the T cell response is unlikely to be feasible in the near term. Focused evaluation in specific sub-groups, including vaccine recipients, should be prioritised.
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Affiliation(s)
- Madhumita Shrotri
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
- National Infection Service, Public Health England, London, United Kingdom
| | - May C. I. van Schalkwyk
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nathan Post
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Danielle Eddy
- National Infection Service, Public Health England, London, United Kingdom
| | - Catherine Huntley
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Leeman
- National Infection Service, Public Health England, London, United Kingdom
| | - Samuel Rigby
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah V. Williams
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - William H. Bermingham
- Department of Clinical Immunology, University Hospitals Birmingham, Birmingham, United Kingdom
| | - Paul Kellam
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - John Maher
- School of Cancer and Pharmaceutical Studies, King’s College London, London, United Kingdom
- Department of Immunology, Eastbourne Hospital, Eastbourne, United Kingdom
| | - Adrian M. Shields
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | | | - Sharon J. Peacock
- National Infection Service, Public Health England, London, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sharif A. Ismail
- National Infection Service, Public Health England, London, United Kingdom
- Department of Primary Care and Public Health, Imperial College London, London, United Kingdom
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, United Kingdom
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380
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da Silva Antunes R, Pallikkuth S, Williams E, Yu ED, Mateus J, Quiambao L, Wang E, Rawlings SA, Stadlbauer D, Jiang K, Amanat F, Arnold D, Andrews D, Fuego I, Dan JM, Grifoni A, Weiskopf D, Krammer F, Crotty S, Hoffer ME, Pahwa SG, Sette A. Differential T cell reactivity to seasonal coronaviruses and SARS-CoV-2 in community and health care workers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.12.21249683. [PMID: 33469594 PMCID: PMC7814840 DOI: 10.1101/2021.01.12.21249683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Herein we measured CD4+ T cell responses against common cold corona (CCC) viruses and SARS-CoV-2 in high-risk health care workers (HCW) and community controls. We observed higher levels of CCC reactive T cells in SARS-CoV-2 seronegative HCW compared to community donors, consistent with potential higher occupational exposure of HCW to CCC. We further show that SARS-CoV-2 reactivity of seronegative HCW was higher than community controls and correlation between CCC and SARS-CoV-2 responses is consistent with cross-reactivity and not associated with recent in vivo activation. Surprisingly, CCC reactivity was decreased in SARS-CoV-2 infected HCW, suggesting that exposure to SARS-CoV-2 might interfere with CCC responses, either directly or indirectly. This result was unexpected, but consistently detected in independent cohorts derived from Miami and San Diego.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Erin Williams
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Lorenzo Quiambao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Eric Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaijun Jiang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Arnold
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - David Andrews
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Irma Fuego
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, 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
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shane Crotty
- 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
| | - Michael E. Hoffer
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Savita G. Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, 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
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381
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Pinotti F, Wikramaratna PS, Obolski U, Paton RS, Damineli DSC, Alcantara LCJ, Giovanetti M, Gupta S, Lourenço J. Potential impact of individual exposure histories to endemic human coronaviruses on age-dependent severity of COVID-19. BMC Med 2021; 19:19. [PMID: 33430856 PMCID: PMC7801230 DOI: 10.1186/s12916-020-01887-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cross-reactivity to SARS-CoV-2 from exposure to endemic human coronaviruses (eHCoV) is gaining increasing attention as a possible driver of both protection against infection and COVID-19 severity. Here we explore the potential role of cross-reactivity induced by eHCoVs on age-specific COVID-19 severity in a mathematical model of eHCoV and SARS-CoV-2 transmission. METHODS We use an individual-based model, calibrated to prior knowledge of eHCoV dynamics, to fully track individual histories of exposure to eHCoVs. We also model the emergent dynamics of SARS-CoV-2 and the risk of hospitalisation upon infection. RESULTS We hypothesise that primary exposure with any eHCoV confers temporary cross-protection against severe SARS-CoV-2 infection, while life-long re-exposure to the same eHCoV diminishes cross-protection, and increases the potential for disease severity. We show numerically that our proposed mechanism can explain age patterns of COVID-19 hospitalisation in EU/EEA countries and the UK. We further show that some of the observed variation in health care capacity and testing efforts is compatible with country-specific differences in hospitalisation rates under this model. CONCLUSIONS This study provides a "proof of possibility" for certain biological and epidemiological mechanisms that could potentially drive COVID-19-related variation across age groups. Our findings call for further research on the role of cross-reactivity to eHCoVs and highlight data interpretation challenges arising from health care capacity and SARS-CoV-2 testing.
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Affiliation(s)
| | | | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Daniel S C Damineli
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz C J Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
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383
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Hanna SJ, Codd AS, Gea-Mallorqui E, Scourfield DO, Richter FC, Ladell K, Borsa M, Compeer EB, Moon OR, Galloway SAE, Dimonte S, Capitani L, Shepherd FR, Wilson JD, Uhl LFK, Gallimore AM, Milicic A. T cell phenotypes in COVID-19 - a living review. OXFORD OPEN IMMUNOLOGY 2020; 2:iqaa007. [PMID: 33575657 PMCID: PMC7798577 DOI: 10.1093/oxfimm/iqaa007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/06/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is characterized by profound lymphopenia in the peripheral blood, and the remaining T cells display altered phenotypes, characterized by a spectrum of activation and exhaustion. However, antigen-specific T cell responses are emerging as a crucial mechanism for both clearance of the virus and as the most likely route to long-lasting immune memory that would protect against re-infection. Therefore, T cell responses are also of considerable interest in vaccine development. Furthermore, persistent alterations in T cell subset composition and function post-infection have important implications for patients' long-term immune function. In this review, we examine T cell phenotypes, including those of innate T cells, in both peripheral blood and lungs, and consider how key markers of activation and exhaustion correlate with, and may be able to predict, disease severity. We focus on SARS-CoV-2-specific T cells to elucidate markers that may indicate formation of antigen-specific T cell memory. We also examine peripheral T cell phenotypes in recovery and the likelihood of long-lasting immune disruption. Finally, we discuss T cell phenotypes in the lung as important drivers of both virus clearance and tissue damage. As our knowledge of the adaptive immune response to COVID-19 rapidly evolves, it has become clear that while some areas of the T cell response have been investigated in some detail, others, such as the T cell response in children remain largely unexplored. Therefore, this review will also highlight areas where T cell phenotypes require urgent characterisation.
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Affiliation(s)
- Stephanie J Hanna
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK,Correspondence address. Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Tel: +44 29206 87342, E-mail:
| | - Amy S Codd
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Ester Gea-Mallorqui
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
| | - D Oliver Scourfield
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Felix C Richter
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, OX3 FTY, UK
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Mariana Borsa
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, OX3 FTY, UK
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, OX3 FTY, UK
| | - Owen R Moon
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sarah A E Galloway
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sandra Dimonte
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Lorenzo Capitani
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Freya R Shepherd
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Joseph D Wilson
- Medical Sciences Division, University of Oxford, Headington, Oxford, OX3 9DU
| | - Lion F K Uhl
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, OX3 FTY, UK
| | | | - Awen M Gallimore
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Anita Milicic
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
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384
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Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.24.424262. [PMID: 33398286 PMCID: PMC7781330 DOI: 10.1101/2020.12.24.424262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
T-cells play an essential role in the adaptive immune system by seeking out, binding and destroying foreign antigens presented on the cell surface of diseased cells. An improved understanding of T-cell immunity will greatly aid in the development of new cancer immunotherapies and vaccines for life threatening pathogens. Central to the design of such targeted therapies are computational methods to predict non-native epitopes to elicit a T cell response, however, we currently lack accurate immunogenicity inference methods. Another challenge is the ability to accurately simulate immunogenic peptides for specific human leukocyte antigen (HLA) alleles, for both synthetic biological applications and to augment real training datasets. Here, we proposed a beta-binomial distribution approach to derive epitope immunogenic potential from sequence alone. We conducted systematic benchmarking of five traditional machine learning (ElasticNet, KNN, SVM, Random Forest, AdaBoost) and three deep learning models (CNN, ResNet, GNN) using three independent prior validated immunogenic peptide collections (dengue virus, cancer neoantigen and SARS-Cov-2). We chose the CNN model as the best prediction model based on its adaptivity for small and large datasets, and performance relative to existing methods. In addition to outperforming two highly used immunogenicity prediction algorithms, DeepHLApan and IEDB, DeepImmuno-CNN further correctly predicts which residues are most important for T cell antigen recognition. Our independent generative adversarial network (GAN) approach, DeepImmuno-GAN, was further able to accurately simulate immunogenic peptides with physiochemical properties and immunogenicity predictions similar to that of real antigens. We provide DeepImmuno-CNN as source code and an easy-to-use web interface. DATA AVAILABILITY DeepImmuno Python3 code is available at https://github.com/frankligy/DeepImmuno . The DeepImmuno web portal is available from https://deepimmuno.herokuapp.com . The data in this article is available in GitHub and supplementary materials.
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Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
| | - Yizhao Ni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
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385
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Reynolds CJ, Swadling L, Gibbons JM, Pade C, Jensen MP, Diniz MO, Schmidt NM, Butler DK, Amin OE, Bailey SNL, Murray SM, Pieper FP, Taylor S, Jones J, Jones M, Lee WYJ, Rosenheim J, Chandran A, Joy G, Di Genova C, Temperton N, Lambourne J, Cutino-Moguel T, Andiapen M, Fontana M, Smit A, Semper A, O'Brien B, Chain B, Brooks T, Manisty C, Treibel T, Moon JC, Noursadeghi M, Altmann DM, Maini MK, McKnight Á, Boyton RJ. Discordant neutralizing antibody and T cell responses in asymptomatic and mild SARS-CoV-2 infection. Sci Immunol 2020; 5:eabf3698. [PMID: 33361161 PMCID: PMC8101131 DOI: 10.1126/sciimmunol.abf3698] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022]
Abstract
Understanding the nature of immunity following mild/asymptomatic infection with SARS-CoV-2 is crucial to controlling the pandemic. We analyzed T cell and neutralizing antibody responses in 136 healthcare workers (HCW) 16-18 weeks after United Kingdom lockdown, 76 of whom had mild/asymptomatic SARS-CoV-2 infection captured by serial sampling. Neutralizing antibodies (nAb) were present in 89% of previously infected HCW. T cell responses tended to be lower following asymptomatic infection than in those reporting case-definition symptoms of COVID-19, while nAb titers were maintained irrespective of symptoms. T cell and antibody responses were sometimes discordant. Eleven percent lacked nAb and had undetectable T cell responses to spike protein but had T cells reactive with other SARS-CoV-2 antigens. Our findings suggest that the majority of individuals with mild or asymptomatic SARS-CoV-2 infection carry nAb complemented by multispecific T cell responses at 16-18 weeks after mild or asymptomatic SARS-CoV-2 infection.
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Affiliation(s)
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Melanie P Jensen
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Mariana O Diniz
- Division of Infection and Immunity, University College London, London, UK
| | - Nathalie M Schmidt
- Division of Infection and Immunity, University College London, London, UK
| | - David K Butler
- Department of Infectious Disease, Imperial College London, London, UK
| | - Oliver E Amin
- Division of Infection and Immunity, University College London, London, UK
| | - Sasha N L Bailey
- Department of Infectious Disease, Imperial College London, London, UK
| | - Sam M Murray
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Stephen Taylor
- National Infection Service, Public Health England, Porton Down, UK
| | - Jessica Jones
- National Infection Service, Public Health England, Porton Down, UK
| | - Meleri Jones
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Wing-Yiu Jason Lee
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London, UK
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London, UK
| | - George Joy
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Cecilia Di Genova
- Viral Pseudotype Unit, Medway School of Pharmacy, Chatham Maritime, Kent, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Chatham Maritime, Kent, UK
| | | | | | - Mervyn Andiapen
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | | | | | - Amanda Semper
- National Infection Service, Public Health England, Porton Down, UK
| | - Ben O'Brien
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- German Heart Centre and Charité University, Berlin, Germany
| | - Benjamin Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Tim Brooks
- National Infection Service, Public Health England, Porton Down, UK
| | - Charlotte Manisty
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, UK
| | - Thomas Treibel
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, UK
| | - James C Moon
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London, UK
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London, UK.
- Lung Division, Royal Brompton & Harefield NHS Foundation Trust, London, UK
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386
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Steiner S, Sotzny F, Bauer S, Na IK, Schmueck-Henneresse M, Corman VM, Schwarz T, Drosten C, Wendering DJ, Behrends U, Volk HD, Scheibenbogen C, Hanitsch LG. HCoV- and SARS-CoV-2 Cross-Reactive T Cells in CVID Patients. Front Immunol 2020; 11:607918. [PMID: 33424856 PMCID: PMC7785785 DOI: 10.3389/fimmu.2020.607918] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/20/2020] [Indexed: 01/08/2023] Open
Abstract
The inability of patients with CVID to mount specific antibody responses to pathogens has raised concerns on the risk and severity of SARS-CoV-2 infection, but there might be a role for protective T cells in these patients. SARS-CoV-2 reactive T cells have been reported for SARS-CoV-2 unexposed healthy individuals. Until now, there is no data on T cell immunity to SARS-CoV-2 infection in CVID. This study aimed to evaluate reactive T cells to human endemic corona viruses (HCoV) and to study pre-existing SARS-CoV-2 reactive T cells in unexposed CVID patients. We evaluated SARS-CoV-2- and HCoV-229E and –OC43 reactive T cells in response to seven peptide pools, including spike and nucleocapsid (NCAP) proteins, in 11 unexposed CVID, 12 unexposed and 11 post COVID-19 healthy controls (HC). We further characterized reactive T cells by IFNγ, TNFα and IL-2 profiles. SARS-CoV-2 spike-reactive CD4+ T cells were detected in 7 of 11 unexposed CVID patients, albeit with fewer multifunctional (IFNγ/TNFα/IL-2) cells than unexposed HC. CVID patients had no SARS-CoV-2 NCAP reactive CD4+ T cells and less reactive CD8+ cells compared to unexposed HC. We observed a correlation between T cell reactivity against spike of SARS-CoV-2 and HCoVs in unexposed, but not post COVID-19 HC, suggesting cross-reactivity. T cell responses in post COVID-19 HC could be distinguished from unexposed HC by higher frequencies of triple-positive NCAP reactive CD4+ T cells. Taken together, SARS-CoV-2 reactive T cells are detectable in unexposed CVID patients albeit with lower recognition frequencies and polyfunctional potential. Frequencies of triple-functional reactive CD4+ cells might provide a marker to distinguish HCoV cross-reactive from SARS-CoV-2 specific T cell responses. Our data provides evidence, that anti-viral T cell immunity is not relevantly impaired in most CVID patients.
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Affiliation(s)
- Sophie Steiner
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Franziska Sotzny
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sandra Bauer
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Il-Kang Na
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité University Medicine Berlin, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité University Medicine Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, and German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Tatjana Schwarz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, and German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, and German Centre for Infection Research (DZIF), Partner Site Charité, Berlin, Germany
| | - Désirée J Wendering
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité University Medicine Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uta Behrends
- Department of Pediatrics, Kinderklinik München Schwabing, StKM GmbH und Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Hans-Dieter Volk
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité University Medicine Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Carmen Scheibenbogen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité University Medicine Berlin, Berlin, Germany
| | - Leif G Hanitsch
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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387
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Shomuradova AS, Vagida MS, Sheetikov SA, Zornikova KV, Kiryukhin D, Titov A, Peshkova IO, Khmelevskaya A, Dianov DV, Malasheva M, Shmelev A, Serdyuk Y, Bagaev DV, Pivnyuk A, Shcherbinin DS, Maleeva AV, Shakirova NT, Pilunov A, Malko DB, Khamaganova EG, Biderman B, Ivanov A, Shugay M, Efimov GA. SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors. Immunity 2020; 53:1245-1257.e5. [PMID: 33326767 PMCID: PMC7664363 DOI: 10.1016/j.immuni.2020.11.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/02/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion or activation of preexisting immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike protein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity.
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Affiliation(s)
- Alina S Shomuradova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Savely A Sheetikov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ksenia V Zornikova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Aleksei Titov
- National Research Center for Hematology, Moscow, Russia
| | | | - Alexandra Khmelevskaya
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Dianov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Malasheva
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Shmelev
- National Research Center for Hematology, Moscow, Russia
| | - Yana Serdyuk
- National Research Center for Hematology, Moscow, Russia
| | - Dmitry V Bagaev
- Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anastasia Pivnyuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitrii S Shcherbinin
- Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Artem Pilunov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Alexander Ivanov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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388
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Channappanavar R, Perlman S. Age-related susceptibility to coronavirus infections: role of impaired and dysregulated host immunity. J Clin Invest 2020; 130:6204-6213. [PMID: 33085654 DOI: 10.1172/jci144115] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human coronaviruses (hCoVs) cause severe respiratory illness in the elderly. Age-related impairments in innate immunity and suboptimal virus-specific T cell and antibody responses are believed to cause severe disease upon respiratory virus infections. This phenomenon has recently received increased attention, as elderly patients are at substantially elevated risk for severe COVID-19 disease and experience increased rates of mortality following SARS-CoV-2 infection compared with younger populations. However, the basis for age-related fatal pneumonia following pathogenic hCoVs is not well understood. In this Review, we provide an overview of our current understanding of hCoV-induced fatal pneumonia in the elderly. We describe host immune response to hCoV infections derived from studies of young and aged animal models and discuss the potential role of age-associated increases in sterile inflammation (inflammaging) and virus-induced dysregulated inflammation in causing age-related severe disease. We also highlight the existing gaps in our knowledge about virus replication and host immune responses to hCoV infection in young and aged individuals.
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Affiliation(s)
- Rudragouda Channappanavar
- Department of Acute and Tertiary Care and.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology and.,Stead Family Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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389
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Urbán S, Paragi G, Burián K, McLean GR, Virok DP. Identification of similar epitopes between severe acute respiratory syndrome coronavirus-2 and Bacillus Calmette-Guérin: potential for cross-reactive adaptive immunity. Clin Transl Immunology 2020; 9:e1227. [PMID: 33318797 PMCID: PMC7724920 DOI: 10.1002/cti2.1227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives Bacillus Calmette–Guérin (BCG) vaccination has been implicated in protection against severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and as a non‐specific immunisation method against the virus. We therefore decided to investigate T‐cell and B‐cell epitopes within the BCG‐Pasteur strain proteome for similarity to immunogenic peptides of SARS‐CoV‐2. Methods We used NetMHC 4.0 and BepiPred 2.0 epitope prediction methods for the analysis of the BCG‐Pasteur proteome to identify similar peptides to established and novel SARS‐CoV‐2 T‐cell and B‐cell epitopes. Results We found 112 BCG MHC‐I‐restricted T‐cell epitopes similar to MHC‐I‐restricted T‐cell SARS‐CoV‐2 epitopes and 690 BCG B‐cell epitopes similar to SARS‐CoV‐2 B‐cell epitopes. The SARS‐CoV‐2 T‐cell epitopes represented 16 SARS‐CoV‐2 proteins, and the SARS‐CoV‐2 B‐cell epitopes represented 5 SARS‐CoV‐2 proteins, including the receptor binding domain of the spike glycoprotein. Conclusion Altogether, our results provide a mechanistic basis for the potential cross‐reactive adaptive immunity that may exist between the two microorganisms.
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Affiliation(s)
- Szabolcs Urbán
- Department of Nuclear Medicine University of Szeged Szeged Hungary
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group University of Szeged Szeged Hungary.,Institute of Physics University of Pecs Pecs Hungary
| | - Katalin Burián
- Department of Medical Microbiology and Immunobiology University of Szeged Szeged Hungary
| | - Gary R McLean
- Cellular and Molecular Immunology Research Centre London Metropolitan University London UK.,National Heart and Lung Institute Imperial College London London UK
| | - Dezső P Virok
- Department of Medical Microbiology and Immunobiology University of Szeged Szeged Hungary
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390
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Tarke A, Sidney J, Kidd CK, Dan JM, Ramirez SI, Yu ED, Mateus J, da Silva Antunes R, Moore E, Rubiro P, Methot N, Phillips E, Mallal S, Frazier A, Rawlings SA, Greenbaum JA, Peters B, Smith DM, Crotty S, Weiskopf D, Grifoni A, Sette A. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33330869 DOI: 10.1101/2020.12.08.416750] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measure virus-specific CD4 + and CD8 + T cells, we studied epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differed for CD4 + T cells, CD8 + T cells, and antibodies. The class I and class II epitopes were combined into new epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4 + and CD8 + T cells.
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391
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Zelba H, Worbs D, Harter J, Pieper N, Kyzirakos-Feger C, Kayser S, Seibold M, Bartsch O, Ködding J, Biskup S. A Highly Specific Assay for the Detection of SARS-CoV-2-Reactive CD4 + and CD8 + T Cells in COVID-19 Patients. THE JOURNAL OF IMMUNOLOGY 2020; 206:580-587. [PMID: 33298615 DOI: 10.4049/jimmunol.2000811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/16/2020] [Indexed: 01/08/2023]
Abstract
Gaining detailed insights into the role of host immune responses in viral clearance is critical for understanding COVID-19 pathogenesis and future treatment strategies. Although studies analyzing humoral immune responses against SARS-CoV-2 were available rather early during the pandemic, cellular immunity came into focus of investigations just recently. For the present work, we have adapted a protocol designed for the detection of rare neoantigen-specific memory T cells in cancer patients for studying cellular immune responses against SARS-CoV-2. Both CD4+ and CD8+ T cells were detected after 6 d of in vitro expansion using overlapping peptide libraries representing the whole viral protein. The assay readout was an intracellular cytokine staining and flow cytometric analysis detecting four functional markers simultaneously (CD154, TNF, IL-2, and IFN-γ). We were able to detect SARS-CoV-2-specific T cells in 10 of 10 COVID-19 patients with mild symptoms. All patients had reactive T cells against at least 1 of 12 analyzed viral Ags, and all patients had Spike-specific T cells. Although some Ags were detected by CD4+ and CD8+ T cells, VME1 was mainly recognized by CD4+ T cells. Strikingly, we were not able to detect SARS-CoV-2-specific T cells in 18 unexposed healthy individuals. When we stimulated the same samples overnight, we measured significant numbers of cytokine-producing cells even in unexposed individuals. Our comparison showed that the stimulation conditions can profoundly impact the activation readout in unexposed individuals. We are presenting a highly specific diagnostic tool for the detection of SARS-CoV-2-reactive T cells.
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392
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Karlsson AC, Humbert M, Buggert M. The known unknowns of T cell immunity to COVID-19. Sci Immunol 2020; 5:5/53/eabe8063. [PMID: 33208380 DOI: 10.1126/sciimmunol.abe8063] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022]
Abstract
Tremendous progress has been made in understanding the role of T cell immunity in acute and convalescent COVID-19 infection. Here we shed light on the "known unknowns" of pre-existing and acquired T cell responses in relation to acute and convalescent SARS-CoV-2 infection.
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Affiliation(s)
- Annika C Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Marion Humbert
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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393
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Bacher P, Rosati E, Esser D, Martini GR, Saggau C, Schiminsky E, Dargvainiene J, Schröder I, Wieters I, Khodamoradi Y, Eberhardt F, Vehreschild MJGT, Neb H, Sonntagbauer M, Conrad C, Tran F, Rosenstiel P, Markewitz R, Wandinger KP, Augustin M, Rybniker J, Kochanek M, Leypoldt F, Cornely OA, Koehler P, Franke A, Scheffold A. Low-Avidity CD4 + T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19. Immunity 2020; 53:1258-1271.e5. [PMID: 33296686 PMCID: PMC7689350 DOI: 10.1016/j.immuni.2020.11.016] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/08/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023]
Abstract
CD4+ T cells reactive against SARS-CoV-2 can be found in unexposed individuals, and these are suggested to arise in response to common cold coronavirus (CCCoV) infection. Here, we utilized SARS-CoV-2-reactive CD4+ T cell enrichment to examine the antigen avidity and clonality of these cells, as well as the relative contribution of CCCoV cross-reactivity. SARS-CoV-2-reactive CD4+ memory T cells were present in virtually all unexposed individuals examined, displaying low functional avidity and multiple, highly variable cross-reactivities that were not restricted to CCCoVs. SARS-CoV-2-reactive CD4+ T cells from COVID-19 patients lacked cross-reactivity to CCCoVs, irrespective of strong memory T cell responses against CCCoV in all donors analyzed. In severe but not mild COVID-19, SARS-CoV-2-specific T cells displayed low functional avidity and clonality, despite increased frequencies. Our findings identify low-avidity CD4+ T cell responses as a hallmark of severe COVID-19 and argue against a protective role for CCCoV-reactive T cells in SARS-CoV-2 infection. Low avidity and broad cross-reactivities of pre-existing SARS-CoV-2 memory T cells Strong CCCoV-specific memory CD4+ T cell responses in all analyzed individuals SARS-CoV-2-specific CD4+ T cells in COVID-19 patients lack cross-reactivity to CCCoVs Low avidity and clonality of SARS-CoV-2-specific T cell responses in severe COVID-19
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Affiliation(s)
- Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
| | - Justina Dargvainiene
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Ina Schröder
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Imke Wieters
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Fabian Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger Neb
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Michael Sonntagbauer
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Claudio Conrad
- Department of Internal Medicine, Hospital of Preetz, Preetz, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany; Department of Internal Medicine I, UKSH Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Robert Markewitz
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Klaus-Peter Wandinger
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Max Augustin
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jan Rybniker
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Matthias Kochanek
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany
| | - Frank Leypoldt
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany; Department of Neurology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Oliver A Cornely
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Clinical Trials Centre Cologne, ZKS Köln, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
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394
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Nerli S, Sgourakis NG. Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens. FRONTIERS IN MEDICAL TECHNOLOGY 2020; 2:553478. [PMID: 35047875 PMCID: PMC8757863 DOI: 10.3389/fmedt.2020.553478] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/07/2020] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2-specific CD4 and CD8 T cells have been shown to be present in individuals with acute, mild, and asymptomatic Coronavirus disease (COVID-19). Toward the development of diagnostic and therapeutic tools to fight COVID-19, it is important to predict and characterize T cell epitopes expressed by SARS-CoV-2. Here, we use RosettaMHC, a comparative modeling approach which leverages existing structures of peptide/MHC complexes available in the Protein Data Bank, to derive accurate 3D models for putative SARS-CoV-2 CD8 epitopes. We outline an application of our method to model 8-10 residue epitopic peptides predicted to bind to the common allele HLA-A*02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). We further compare electrostatic surfaces with models of homologous peptide/HLA-A*02:01 complexes from human common cold coronavirus strains to identify epitopes which may be recognized by a shared pool of cross-reactive TCRs. As more detailed studies on antigen-specific T cell recognition become available, RosettaMHC models can be used to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection.
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Affiliation(s)
- Santrupti Nerli
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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395
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Lee CH, Pinho MP, Buckley PR, Woodhouse IB, Ogg G, Simmons A, Napolitani G, Koohy H. Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains. Front Immunol 2020; 11:579480. [PMID: 33250893 PMCID: PMC7676914 DOI: 10.3389/fimmu.2020.579480] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariana Pereira Pinho
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul R. Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Isaac B. Woodhouse
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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396
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Stervbo U, Rahmann S, Roch T, Westhoff TH, Babel N. Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins. Sci Rep 2020; 10:18995. [PMID: 33149224 PMCID: PMC7642385 DOI: 10.1038/s41598-020-75972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023] Open
Abstract
The current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019. Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts studies showing that biobanked venous blood contains T cells reactive to SARS-CoV-2 S-protein even before the outbreak in Wuhan. This suggests a preformed T cell memory towards structural proteins in individuals not exposed to SARS-CoV-2. Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory. However, given the apparent poor immunological memory created by the endemic coronaviruses, immunity against other common pathogens might offer an alternative explanation. Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory. Although beta-coronaviruses are the most likely candidates to explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals, the SARS-CoV-2 epitopes with the highest similarity to those from beta-coronaviruses are confined to replication associated proteins-not the host interacting S-protein. Thus, our study suggests that the observed SARS-CoV-2 pre-formed immunity to structural proteins is not driven by near-identical epitopes.
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Affiliation(s)
- Ulrik Stervbo
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Duisburg, Germany.
| | - Toralf Roch
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Nina Babel
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
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397
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398
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Sauer K, Harris T. An Effective COVID-19 Vaccine Needs to Engage T Cells. Front Immunol 2020; 11:581807. [PMID: 33117391 PMCID: PMC7549399 DOI: 10.3389/fimmu.2020.581807] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/27/2020] [Indexed: 12/28/2022] Open
Affiliation(s)
- Karsten Sauer
- Repertoire Immune Medicines, Cambridge, MA, United States
| | - Tim Harris
- Repertoire Immune Medicines, Cambridge, MA, United States
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