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Vránová L, Poláková I, Vaníková Š, Saláková M, Musil J, Vaníčková M, Vencálek O, Holub M, Bohoněk M, Řezáč D, Dresler J, Tachezy R, Šmahel M. Multiparametric analysis of the specific immune response against SARS-CoV-2. Infect Dis (Lond) 2024:1-19. [PMID: 38805304 DOI: 10.1080/23744235.2024.2358379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND SARS-CoV-2, which causes COVID-19, has killed more than 7 million people worldwide. Understanding the development of postinfectious and postvaccination immune responses is necessary for effective treatment and the introduction of appropriate antipandemic measures. OBJECTIVES We analysed humoral and cell-mediated anti-SARS-CoV-2 immune responses to spike (S), nucleocapsid (N), membrane (M), and open reading frame (O) proteins in individuals collected up to 1.5 years after COVID-19 onset and evaluated immune memory. METHODS Peripheral blood mononuclear cells and serum were collected from patients after COVID-19. Sampling was performed in two rounds: 3-6 months after infection and after another year. Most of the patients were vaccinated between samplings. SARS-CoV-2-seronegative donors served as controls. ELISpot assays were used to detect SARS-CoV-2-specific T and B cells using peptide pools (S, NMO) or recombinant proteins (rS, rN), respectively. A CEF peptide pool consisting of selected viral epitopes was applied to assess the antiviral T-cell response. SARS-CoV-2-specific antibodies were detected via ELISA and a surrogate virus neutralisation assay. RESULTS We confirmed that SARS-CoV-2 infection induces the establishment of long-term memory IgG+ B cells and memory T cells. We also found that vaccination enhanced the levels of anti-S memory B and T cells. Multivariate comparison also revealed the benefit of repeated vaccination. Interestingly, the T-cell response to CEF was lower in patients than in controls. CONCLUSION This study supports the importance of repeated vaccination for enhancing immunity and suggests a possible long-term perturbation of the overall antiviral immune response caused by SARS-CoV-2 infection.
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Affiliation(s)
- Lucie Vránová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Poláková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Šárka Vaníková
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Martina Saláková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Jan Musil
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Marie Vaníčková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ondřej Vencálek
- Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Military University Hospital Prague and Charles University, Prague, Czech Republic
| | - Miloš Bohoněk
- Department of Hematology and Blood Transfusion, Military University Hospital Prague, Prague, Czech Republic
- Faculty of Biomedical Engineering, Czech Technical University, Prague, Czech Republic
| | - David Řezáč
- Department of Infectious Diseases, First Faculty of Medicine, Military University Hospital Prague and Charles University, Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michal Šmahel
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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Oishi T, Yasui Y, Kato A, Ogita S, Eitoku T, Enoki H, Nakano T. Analysis of Cell Immunity for Children Infected with SARS-CoV-2 and Those Vaccinated against SARS-CoV-2 Using T-SPOT ®.COVID. Microorganisms 2024; 12:975. [PMID: 38792804 PMCID: PMC11124318 DOI: 10.3390/microorganisms12050975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Cellular immunity is critical for the regulation of viral diseases, including coronavirus disease 2019 (COVID-19), and is generally considered immature in childhood. However, the details of cellular immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among children are unclear. We assessed cellular immunity in eight children post-vaccination against SARS-CoV-2 and 11 children after SARS-CoV-2 infection using the T-SPOT®.COVID assay for the spike (S) and nucleocapsid (N) proteins. In the vaccinated group, the T-SPOT®.COVID assay for the S protein yielded positive results in seven children. In the post-infection group, the assay for the N protein was positive for 5 of 11 children, with 3 of these 5 children requiring hospitalization, including 2 who needed mechanical ventilation. The T-SPOT®.COVID assay is thus valuable for assessing cellular immunity against SARS-CoV-2, and most children infected with SARS-CoV-2 may not develop such immunity unless the disease severity is significant.
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Affiliation(s)
- Tomohiro Oishi
- Department of Clinical Infectious Diseases, Kawasaki Medical School, 577, Matsushima, Kurashiki 701-0192, Okayama, Japan
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3
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Lu X, Hayashi H, Ishikawa E, Takeuchi Y, Dychiao JVT, Nakagami H, Yamasaki S. Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies. eLife 2024; 12:RP89999. [PMID: 38716629 PMCID: PMC11078543 DOI: 10.7554/elife.89999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) αβ sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as 'sustainers'), but not in 'decliners'. Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic microbes. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.
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Affiliation(s)
- Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
| | - Hiroki Hayashi
- Department of Health Development and Medicine, Osaka University Graduate School of MedicineSuitaJapan
| | - Eri Ishikawa
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
| | - Yukiko Takeuchi
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
| | | | - Hironori Nakagami
- Department of Health Development and Medicine, Osaka University Graduate School of MedicineSuitaJapan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
- Center for Infectious Disease Education and Research (CiDER), Osaka UniversitySuitaJapan
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4
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Bricio-Moreno L, Barreto de Albuquerque J, Neary JM, Nguyen T, Kuhn LF, Yeung Y, Hastie KM, Landeras-Bueno S, Olmedillas E, Hariharan C, Nathan A, Getz MA, Gayton AC, Khatri A, Gaiha GD, Ollmann Saphire E, Luster AD, Moon JJ. Identification of mouse CD4 + T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers. Front Immunol 2024; 15:1329846. [PMID: 38529279 PMCID: PMC10961420 DOI: 10.3389/fimmu.2024.1329846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/29/2024] [Indexed: 03/27/2024] Open
Abstract
Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4+ T cells play an integral role in this process primarily by generating antiviral cytokines and providing help to antibody-producing B cells. To empower detailed studies of SARS-CoV-2-specific CD4+ T cell responses in mouse models, we comprehensively mapped I-Ab-restricted epitopes for the spike and nucleocapsid proteins of the BA.1 variant of concern via IFNγ ELISpot assay. This was followed by the generation of corresponding peptide:MHCII tetramer reagents to directly stain epitope-specific T cells. Using this rigorous validation strategy, we identified 6 immunogenic epitopes in spike and 3 in nucleocapsid, all of which are conserved in the ancestral Wuhan strain. We also validated a previously identified epitope from Wuhan that is absent in BA.1. These epitopes and tetramers will be invaluable tools for SARS-CoV-2 antigen-specific CD4+ T cell studies in mice.
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Affiliation(s)
- Laura Bricio-Moreno
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Juliana Barreto de Albuquerque
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Jake M. Neary
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
| | - Thao Nguyen
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
| | - Lucy F. Kuhn
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
| | - YeePui Yeung
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
| | - Kathryn M. Hastie
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sara Landeras-Bueno
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Eduardo Olmedillas
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Chitra Hariharan
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Anusha Nathan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, United States
| | - Matthew A. Getz
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Alton C. Gayton
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Ashok Khatri
- Harvard Medical School, Boston, MA, United States
- Endocrine Division, MGH, Boston, MA, United States
| | - Gaurav D. Gaiha
- Harvard Medical School, Boston, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- Division of Gastroenterology, MGH, Boston, MA, United States
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Andrew D. Luster
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - James J. Moon
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, MGH, Boston, MA, United States
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5
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Liu Z, Li J, Pei S, Lu Y, Li C, Zhu J, Chen R, Wang D, Sun J, Chen K. An updated review of epidemiological characteristics, immune escape, and therapeutic advances of SARS-CoV-2 Omicron XBB.1.5 and other mutants. Front Cell Infect Microbiol 2023; 13:1297078. [PMID: 38156316 PMCID: PMC10752979 DOI: 10.3389/fcimb.2023.1297078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
The rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the emergence of new variants with different genetic profiles, with important implications for public health. The continued emergence of new variants with unique genetic features and potential changes in biological properties poses significant challenges to public health strategies, vaccine development, and therapeutic interventions. Omicron variants have attracted particular attention due to their rapid spread and numerous mutations in key viral proteins. This review aims to provide an updated and comprehensive assessment of the epidemiological characteristics, immune escape potential, and therapeutic advances of the SARS-CoV-2 Omicron XBB.1.5 variant, as well as other variants.
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Affiliation(s)
- Zongming Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shanshan Pei
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- School of Pharmacy, Beihua University, Jilin, China
| | - Ying Lu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Chaonan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Ruyi Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Di Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jingbo Sun
- School of Pharmacy, Beihua University, Jilin, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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Yu H, Guan F, Miller H, Lei J, Liu C. The role of SARS-CoV-2 nucleocapsid protein in antiviral immunity and vaccine development. Emerg Microbes Infect 2023; 12:e2164219. [PMID: 36583642 PMCID: PMC9980416 DOI: 10.1080/22221751.2022.2164219] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ABSTRACTThe coronavirus disease 2019 (COVID-19) has caused enormous health risks and global economic disruption. This disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 nucleocapsid protein is a structural protein involved in viral replication and assembly. There is accumulating evidence indicating that the nucleocapsid protein is multi-functional, playing a key role in the pathogenesis of COVID-19 and antiviral immunity against SARS-CoV-2. Here, we summarize its potential application in the prevention of COVID-19, which is based on its role in inflammation, cell death, antiviral innate immunity, and antiviral adaptive immunity.
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Affiliation(s)
- Haiyun Yu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Heather Miller
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China, Chaohong Liu
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7
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Kim IS, Kang CK, Lee SJ, Lee CH, Kim M, Seo C, Kim G, Lee S, Park KS, Chang E, Jung J, Song KH, Choe PG, Park WB, Kim ES, Bin Kim H, Kim NJ, Oh MD, Lee JE, Shin HM, Kim HR. Tracking antigen-specific TCR clonotypes in SARS-CoV-2 infection reveals distinct severity trajectories. J Med Virol 2023; 95:e29199. [PMID: 37916645 DOI: 10.1002/jmv.29199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Despite the importance of antigen-specific T cells in infectious disease, characterizing and tracking clonally amplified T cells during the progression of a patient's symptoms remain unclear. Here, we performed a longitudinal, in-depth single-cell multiomics analysis of samples from asymptomatic, mild, usual severe, and delayed severe patients of SARS-CoV-2 infection. Our in-depth analysis revealed that hyperactive or improper T-cell responses were more aggressive in delayed severe patients. Interestingly, tracking of antigen-specific T-cell receptor (TCR) clonotypes along the developmental trajectory indicated an attenuation in functional T cells upon severity. In addition, increased glycolysis and interleukin-6 signaling in the cytotoxic T cells were markedly distinct in delayed severe patients compared to usual severe patients, particularly in the middle and late stages of infection. Tracking B-cell receptor clonotypes also revealed distinct transitions and somatic hypermutations within B cells across different levels of disease severity. Our results suggest that single-cell TCR clonotype tracking can distinguish the severity of patients through immunological hallmarks, leading to a better understanding of the severity differences in and improving the management of infectious diseases by analyzing the dynamics of immune responses over time.
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Affiliation(s)
- Ik Soo Kim
- Department of Microbiology, Gachon University College of Medicine, Incheon, South Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Chang-Han Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Minji Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Gwanghun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Soojin Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyoung Sun Park
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jongtak Jung
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Hyun Mu Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hang-Rae Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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Dang TTT, Anzurez A, Nakayama-Hosoya K, Miki S, Yamashita K, de Souza M, Matano T, Kawana-Tachikawa A. Breadth and Durability of SARS-CoV-2-Specific T Cell Responses following Long-Term Recovery from COVID-19. Microbiol Spectr 2023; 11:e0214323. [PMID: 37428088 PMCID: PMC10433967 DOI: 10.1128/spectrum.02143-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
T cell immunity is crucial for long-term immunological memory, but the profile of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific memory T cells in individuals who recovered from COVID-19 (COVID-19-convalescent individuals) is not sufficiently assessed. In this study, the breadth and magnitude of SARS-CoV-2-specific T cell responses were determined in COVID-19-convalescent individuals in Japan. Memory T cells against SARS-CoV-2 were detected in all convalescent individuals, and those with more severe disease exhibited a broader T cell response relative to cases with mild symptoms. Comprehensive screening of T cell responses at the peptide level was conducted for spike (S) and nucleocapsid (N) proteins, and regions frequently targeted by T cells were identified. Multiple regions in S and N proteins were targeted by memory T cells, with median numbers of target regions of 13 and 4, respectively. A maximum of 47 regions were recognized by memory T cells for an individual. These data indicate that SARS-CoV-2-convalescent individuals maintain a substantial breadth of memory T cells for at least several months following infection. Broader SARS-CoV-2-specific CD4+ T cell responses, relative to CD8+ T cell responses, were observed for the S but not the N protein, suggesting that antigen presentation is different between viral proteins. The binding affinity of predicted CD8+ T cell epitopes to HLA class I molecules in these regions was preserved for the Delta variant and at 94 to 96% for SARS-CoV-2 Omicron subvariants, suggesting that the amino acid changes in these variants do not have a major impact on antigen presentation to SARS-CoV-2-specific CD8+ T cells. IMPORTANCE RNA viruses, including SARS-CoV-2, evade host immune responses through mutations. As broader T cell responses against multiple viral proteins could minimize the impact of each single amino acid mutation, the breadth of memory T cells would be one essential parameter for effective protection. In this study, breadth of memory T cells to S and N proteins was assessed in COVID-19-convalescent individuals. While broad T cell responses were induced against both proteins, the ratio of N to S proteins for breadth of T cell responses was significantly higher in milder cases. The breadth of CD4+ and CD8+ T cell responses was also significantly different between S and N proteins, suggesting different contributions of N and S protein-specific T cells for COVID-19 control. Most CD8+ T cell epitopes in the immunodominant regions maintained their HLA binding to SARS-CoV-2 Omicron subvariants. Our study provides insights into understanding the protective efficacy of SARS-CoV-2-specific memory T cells against reinfection.
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Affiliation(s)
- Thi Thu Thao Dang
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Alitzel Anzurez
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | | | - Shoji Miki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Mark de Souza
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Jonny J, Putranto TA, Yana ML, Sitepu EC, Irfon R, Ramadhani BP, Sofro MAU, Nency YM, Lestari ES, Triwardhani R, Mujahidah, Sari RK, Soetojo NA. Safety and efficacy of dendritic cell vaccine for COVID-19 prevention after 1-Year follow-up: phase I and II clinical trial final result. Front Immunol 2023; 14:1122389. [PMID: 37404828 PMCID: PMC10315914 DOI: 10.3389/fimmu.2023.1122389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/24/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction Interim analysis of phase I and phase II clinical trials of personalized vaccines made from autologous monocyte-derived dendritic cells (DCs) incubated with S-protein of SARS-CoV-2 show that this vaccine is safe and well tolerated. Our previous report also indicates that this vaccine can induce specific T-cell and B cell responses against SARS-CoV-2. Herein, we report the final analysis after 1 year of follow-up regarding its safety and efficacy in subjects of phase I and phase II clinical trials. Methods Adult subjects (>18 years old) were given autologous DCs derived from peripheral blood monocytes, which were incubated with the S-protein of SARS-CoV-2. The primary outcome is safety in phase I clinical trials. Meanwhile, optimal antigen dosage is determined in phase II clinical trials. Corona Virus Disease 2019 (COVID-19) and Non-COVID-19 adverse events (AEs) were observed for 1 year. Results A total of 28 subjects in the phase I clinical trial were randomly assigned to nine groups based on antigen and Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) dosage. In the phase II clinical trial, 145 subjects were randomly grouped into three groups based on antigen dosage. During the 1-year follow-up period, 35.71% of subjects in phase I and 16.54% in phase II had non-COVID AEs. No subjects in phase I experienced moderate-severe COVID-19. Meanwhile, 4.31% of subjects in phase II had moderate-severe COVID-19. There is no difference in both COVID and non-COVID-19 AEs between groups. Conclusions After 1 year of follow-up, this vaccine is proven safe and effective for preventing COVID-19. A phase III clinical trial involving more subjects should be conducted to establish its efficacy and see other possible side effects.
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Affiliation(s)
- Jonny Jonny
- Installation of Cellcure Development, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
- Faculty of Medicine University of Pembangunan Nasional “Veteran” Jakarta, Jakarta, Indonesia
| | - Terawan Agus Putranto
- Installation of Cellcure Development, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
| | - Martina Lily Yana
- Installation of Cellcure Development, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
| | - Enda Cindylosa Sitepu
- Installation of Cellcure Development, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
| | - Raoulian Irfon
- Installation of Cellcure Development, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
| | | | | | - Yetty Movieta Nency
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Endang Sri Lestari
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Ria Triwardhani
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Mujahidah
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Retty Karisma Sari
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Nur Alaydrus Soetojo
- Dr. Kariadi Hospital/Faculty of Medicine, Diponegoro University, Semarang, Indonesia
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10
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Gray-Gaillard SL, Solis S, Chen HM, Monteiro C, Ciabattoni G, Samanovic MI, Cornelius AR, Williams T, Geesey E, Rodriguez M, Ortigoza MB, Ivanova EN, Koralov SB, Mulligan MJ, Herati RS. Inflammation durably imprints memory CD4+ T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.11.15.516351. [PMID: 36415470 PMCID: PMC9681040 DOI: 10.1101/2022.11.15.516351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs when primed in these two contexts. Notably, viral infection is generally associated with higher levels of systemic inflammation than is vaccination. To assess whether the inflammatory milieu at the time of CD4+ T cell priming has long-term effects on memory, we compared Spike-specific memory CD4+ T cells in 22 individuals around the time of the participants' third SARS-CoV-2 mRNA vaccination, with stratification by whether the participants' first exposure to Spike was via virus or mRNA vaccine. Multimodal single-cell profiling of Spike-specific CD4+ T cells revealed 755 differentially expressed genes that distinguished infection- and vaccine-primed memory CD4+ T cells. Spike-specific CD4+ T cells from infection-primed individuals had strong enrichment for cytotoxicity and interferon signaling genes, whereas Spike-specific CD4+ T cells from vaccine-primed individuals were enriched for proliferative pathways by gene set enrichment analysis. Moreover, Spike-specific memory CD4+ T cells established by infection had distinct epigenetic landscapes driven by enrichment of IRF-family transcription factors, relative to T cells established by mRNA vaccination. This transcriptional imprint was minimally altered following subsequent mRNA vaccination or breakthrough infection, reflecting the strong bias induced by the inflammatory environment during initial memory differentiation. Together, these data suggest that the inflammatory context during CD4+ T cell priming is durably imprinted in the memory state at transcriptional and epigenetic levels, which has implications for personalization of vaccination based on prior infection history.
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Affiliation(s)
| | - Sabrina Solis
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Han M. Chen
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Clarice Monteiro
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Grace Ciabattoni
- Department of Microbiology, New York University School of Medicine; New York, NY, USA
| | - Marie I. Samanovic
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Amber R. Cornelius
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Tijaana Williams
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Emilie Geesey
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Miguel Rodriguez
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Mila Brum Ortigoza
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
| | - Ellie N. Ivanova
- Department of Pathology, New York University School of Medicine; New York, NY, USA
| | - Sergei B. Koralov
- Department of Pathology, New York University School of Medicine; New York, NY, USA
| | - Mark J. Mulligan
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
- Department of Microbiology, New York University School of Medicine; New York, NY, USA
| | - Ramin Sedaghat Herati
- Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA
- Department of Microbiology, New York University School of Medicine; New York, NY, USA
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11
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Sunagar R, Singh A, Kumar S. SARS-CoV-2: Immunity, Challenges with Current Vaccines, and a Novel Perspective on Mucosal Vaccines. Vaccines (Basel) 2023; 11:vaccines11040849. [PMID: 37112761 PMCID: PMC10143972 DOI: 10.3390/vaccines11040849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The global rollout of COVID-19 vaccines has played a critical role in reducing pandemic spread, disease severity, hospitalizations, and deaths. However, the first-generation vaccines failed to block severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission, partially due to the limited induction of mucosal immunity, leading to the continuous emergence of variants of concern (VOC) and breakthrough infections. To meet the challenges from VOC, limited durability, and lack of mucosal immune response of first-generation vaccines, novel approaches are being investigated. Herein, we have discussed the current knowledge pertaining to natural and vaccine-induced immunity, and the role of the mucosal immune response in controlling SARS-CoV2 infection. We have also presented the current status of the novel approaches aimed at eliciting both mucosal and systemic immunity. Finally, we have presented a novel adjuvant-free approach to elicit effective mucosal immunity against SARS-CoV-2, which lacks the safety concerns associated with live-attenuated vaccine platforms.
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Affiliation(s)
| | - Amit Singh
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Sudeep Kumar
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
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12
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Yu M, Charles A, Cagigi A, Christ W, Österberg B, Falck-Jones S, Azizmohammadi L, Åhlberg E, Falck-Jones R, Svensson J, Nie M, Warnqvist A, Hellgren F, Lenart K, Arcoverde Cerveira R, Ols S, Lindgren G, Lin A, Maecker H, Bell M, Johansson N, Albert J, Sundling C, Czarnewski P, Klingström J, Färnert A, Loré K, Smed-Sörensen A. Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19. Nat Commun 2023; 14:2164. [PMID: 37061513 PMCID: PMC10105364 DOI: 10.1038/s41467-023-37835-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.
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Affiliation(s)
- Meng Yu
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Alberto Cagigi
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Wanda Christ
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Björn Österberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Falck-Jones
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lida Azizmohammadi
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eric Åhlberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ryan Falck-Jones
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Julia Svensson
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mu Nie
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Warnqvist
- Division of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fredrika Hellgren
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Klara Lenart
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rodrigo Arcoverde Cerveira
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Ols
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Lindgren
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ang Lin
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Holden Maecker
- The Human Immune Monitoring Center, Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Bell
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Niclas Johansson
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Jonas Klingström
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Karin Loré
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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13
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Immune Dynamics Involved in Acute and Convalescent COVID-19 Patients. IMMUNO 2023. [DOI: 10.3390/immuno3010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
COVID-19 is a viral disease that has caused millions of deaths around the world since 2020. Many strategies have been developed to manage patients in critical conditions; however, comprehension of the immune system is a key factor in viral clearance, tissue repairment, and adaptive immunity stimulus. Participation of immunity has been identified as a major factor, along with biomarkers, prediction of clinical outcomes, and antibody production after infection. Immune cells have been proposed not only as a hallmark of severity, but also as a predictor of clinical outcomes, while dynamics of inflammatory molecules can also induce worse consequences for acute patients. For convalescent patients, mild disease was related to higher antibody production, although the factors related to the specific antibodies based on a diversity of antigens were not clear. COVID-19 was explored over time; however, the study of immunological predictors of outcomes is still lacking discussion, especially in convalescent patients. Here, we propose a review using previously published studies to identify immunological markers of COVID-19 outcomes and their relation to antibody production to further contribute to the clinical and laboratorial management of patients.
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14
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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15
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Luxenburger H, Reeg DB, Lang-Meli J, Reinscheid M, Eisner M, Bettinger D, Oberhardt V, Salimi Alizei E, Wild K, Graeser A, Karl V, Sagar, Emmerich F, Klein F, Panning M, Huzly D, Bengsch B, Boettler T, Elling R, Thimme R, Hofmann M, Neumann-Haefelin C. Boosting compromised SARS-CoV-2-specific immunity with mRNA vaccination in liver transplant recipients. J Hepatol 2023; 78:1017-1027. [PMID: 36804404 PMCID: PMC10019593 DOI: 10.1016/j.jhep.2023.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/10/2023] [Accepted: 02/04/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND & AIMS Liver transplant recipients (LTRs) demonstrate a reduced response to COVID-19 mRNA vaccination; however, a detailed understanding of the interplay between humoral and cellular immunity, especially after a third (and fourth) vaccine dose, is lacking. METHODS We longitudinally compared the humoral, as well as CD4+ and CD8+ T-cell, responses between LTRs (n = 24) and healthy controls (n = 19) after three (LTRs: n = 9 to 16; healthy controls: n = 9 to 14 per experiment) to four (LTRs: n = 4; healthy controls: n = 4) vaccine doses, including in-depth phenotypical and functional characterization. RESULTS Compared to healthy controls, development of high antibody titers required a third vaccine dose in most LTRs, while spike-specific CD8+ T cells with robust recall capacity plateaued after the second vaccine dose, albeit with a reduced frequency and epitope repertoire compared to healthy controls. This overall attenuated vaccine response was linked to a reduced frequency of spike-reactive follicular T helper cells in LTRs. CONCLUSION Three doses of a COVID-19 mRNA vaccine induce an overall robust humoral and cellular memory response in most LTRs. Decisions regarding additional booster doses may thus be based on individual vaccine responses as well as evolution of novel variants of concern. IMPACT AND IMPLICATIONS Due to immunosuppressive medication, liver transplant recipients (LTR) display reduced antibody titers upon COVID-19 mRNA vaccination, but the impact on long-term immune memory is not clear. Herein, we demonstrate that after three vaccine doses, the majority of LTRs not only exhibit substantial antibody titers, but also a robust memory T-cell response. Additional booster vaccine doses may be of special benefit for a small subset of LTRs with inferior vaccine response and may provide superior protection against evolving novel viral variants. These findings will help physicians to guide LTRs regarding the benefit of booster vaccinations.
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Affiliation(s)
- Hendrik Luxenburger
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; IMM-PACT, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - David B Reeg
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Lang-Meli
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; IMM-PACT, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Reinscheid
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Miriam Eisner
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106, Freiburg, Germany
| | - Dominik Bettinger
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Valerie Oberhardt
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elahe Salimi Alizei
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Wild
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne Graeser
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vivien Karl
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sagar
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Florian Emmerich
- Institute for Transfusion Medicine and Gene Therapy, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Bengsch
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roland Elling
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Christoph Neumann-Haefelin
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Jeyananthan P. Role of different types of RNA molecules in the severity prediction of SARS-CoV-2 patients. Pathol Res Pract 2023; 242:154311. [PMID: 36657221 PMCID: PMC9840815 DOI: 10.1016/j.prp.2023.154311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/16/2023]
Abstract
SARS-CoV-2 pandemic is the current threat of the world with enormous number of deceases. As most of the countries have constraints on resources, particularly for intensive care and oxygen, severity prediction with high accuracy is crucial. This prediction will help the medical society in the selection of patients with the need for these constrained resources. Literature shows that using clinical data in this study is the common trend and molecular data is rarely utilized in this prediction. As molecular data carry more disease related information, in this study, three different types of RNA molecules ( lncRNA, miRNA and mRNA) of SARS-COV-2 patients are used to predict the severity stage and treatment stage of those patients. Using seven different machine learning algorithms along with several feature selection techniques shows that in both phenotypes, feature importance selected features provides the best accuracy along with random forest classifier. Further to this, it shows that in the severity stage prediction miRNA and lncRNA give the best performance, and lncRNA data gives the best in treatment stage prediction. As most of the studies related to molecular data uses mRNA data, this is an interesting finding.
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17
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Almendro-Vázquez P, Laguna-Goya R, Paz-Artal E. Defending against SARS-CoV-2: The T cell perspective. Front Immunol 2023; 14:1107803. [PMID: 36776863 PMCID: PMC9911802 DOI: 10.3389/fimmu.2023.1107803] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2-specific T cell response has been proven essential for viral clearance, COVID-19 outcome and long-term memory. Impaired early T cell-driven immunity leads to a severe form of the disease associated with lymphopenia, hyperinflammation and imbalanced humoral response. Analyses of acute SARS-CoV-2 infection have revealed that mild COVID-19 course is characterized by an early induction of specific T cells within the first 7 days of symptoms, coordinately followed by antibody production for an effective control of viral infection. In contrast, patients who do not develop an early specific cellular response and initiate a humoral immune response with subsequent production of high levels of antibodies, develop severe symptoms. Yet, delayed and persistent bystander CD8+ T cell activation has been also reported in hospitalized patients and could be a driver of lung pathology. Literature supports that long-term maintenance of T cell response appears more stable than antibody titters. Up to date, virus-specific T cell memory has been detected 22 months post-symptom onset, with a predominant IL-2 memory response compared to IFN-γ. Furthermore, T cell responses are conserved against the emerging variants of concern (VoCs) while these variants are mostly able to evade humoral responses. This could be partly explained by the high HLA polymorphism whereby the viral epitope repertoire recognized could differ among individuals, greatly decreasing the likelihood of immune escape. Current COVID-19-vaccination has been shown to elicit Th1-driven spike-specific T cell response, as does natural infection, which provides substantial protection against severe COVID-19 and death. In addition, mucosal vaccination has been reported to induce strong adaptive responses both locally and systemically and to protect against VoCs in animal models. The optimization of vaccine formulations by including a variety of viral regions, innovative adjuvants or diverse administration routes could result in a desirable enhanced cellular response and memory, and help to prevent breakthrough infections. In summary, the increasing evidence highlights the relevance of monitoring SARS-CoV-2-specific cellular immune response, and not only antibody levels, as a correlate for protection after infection and/or vaccination. Moreover, it may help to better identify target populations that could benefit most from booster doses and to personalize vaccination strategies.
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Affiliation(s)
- Patricia Almendro-Vázquez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rocío Laguna-Goya
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
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18
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Hu H, Feng Z, Lin H, Zhao J, Zhang Y, Xu F, Chen L, Chen F, Ma Y, Su J, Zhao Q, Shuai J. Modeling and analyzing single-cell multimodal data with deep parametric inference. Brief Bioinform 2023; 24:6987655. [PMID: 36642414 DOI: 10.1093/bib/bbad005] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/11/2022] [Accepted: 01/02/2023] [Indexed: 01/17/2023] Open
Abstract
The proliferation of single-cell multimodal sequencing technologies has enabled us to understand cellular heterogeneity with multiple views, providing novel and actionable biological insights into the disease-driving mechanisms. Here, we propose a comprehensive end-to-end single-cell multimodal analysis framework named Deep Parametric Inference (DPI). DPI transforms single-cell multimodal data into a multimodal parameter space by inferring individual modal parameters. Analysis of cord blood mononuclear cells (CBMC) reveals that the multimodal parameter space can characterize the heterogeneity of cells more comprehensively than individual modalities. Furthermore, comparisons with the state-of-the-art methods on multiple datasets show that DPI has superior performance. Additionally, DPI can reference and query cell types without batch effects. As a result, DPI can successfully analyze the progression of COVID-19 disease in peripheral blood mononuclear cells (PBMC). Notably, we further propose a cell state vector field and analyze the transformation pattern of bone marrow cells (BMC) states. In conclusion, DPI is a powerful single-cell multimodal analysis framework that can provide new biological insights into biomedical researchers. The python packages, datasets and user-friendly manuals of DPI are freely available at https://github.com/studentiz/dpi.
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Affiliation(s)
- Huan Hu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China.,National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361005 China.,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), and Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Zhen Feng
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou 325000, China
| | - Hai Lin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), and Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junjie Zhao
- Cyberspace Institute of Advanced Technology, Guangzhou University, Guangzhou 510000, China
| | - Yaru Zhang
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China
| | - Fei Xu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Lingling Chen
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Feng Chen
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Yunlong Ma
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Jianwei Shuai
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China.,National Institute for Data Science in Health and Medicine, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361005 China.,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), and Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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19
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Chen Y, Tong P, Whiteman N, Moghaddam AS, Zarghami M, Zuiani A, Habibi S, Gautam A, Keerti F, Bi C, Xiao T, Cai Y, Chen B, Neuberg D, Wesemann DR. Immune recall improves antibody durability and breadth to SARS-CoV-2 variants. Sci Immunol 2022; 7:eabp8328. [PMID: 35549298 PMCID: PMC9097880 DOI: 10.1126/sciimmunol.abp8328] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/06/2022] [Indexed: 01/11/2023]
Abstract
Key features of immune memory are greater and faster antigen-specific antibody responses to repeat infection. In the setting of immune-evading viral evolution, it is important to understand how far antibody memory recognition stretches across viral variants when memory cells are recalled to action by repeat invasions. It is also important to understand how immune recall influences longevity of secreted antibody responses. We analyzed SARS-CoV-2 variant recognition; dynamics of memory B cells; and secreted antibody over time after infection, vaccination, and boosting. We find that a two-dose SARS-CoV-2 vaccination regimen given after natural infection generated greater longitudinal antibody stability and induced maximal antibody magnitudes with enhanced breadth across Beta, Gamma, Delta and Omicron variants. A homologous third messenger RNA vaccine dose in COVID-naïve individuals conferred greater cross-variant evenness of neutralization potency with stability that was equal to the hybrid immunity conferred by infection plus vaccination. Within unvaccinated individuals who recovered from COVID, enhanced antibody stability over time was observed within a subgroup of individuals who recovered more quickly from COVID and harbored significantly more memory B cells cross-reactive to endemic coronaviruses early after infection. These cross-reactive clones map to the conserved S2 region of SARS-CoV-2 spike with higher somatic hypermutation levels and greater target affinity. We conclude that SARS-CoV-2 antigen challenge histories in humans influence not only the speed and magnitude of antibody responses but also functional cross-variant antibody repertoire composition and longevity.
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Affiliation(s)
- Yuezhou Chen
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Pei Tong
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Noah Whiteman
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Ali Sanjari Moghaddam
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Mehrdad Zarghami
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Adam Zuiani
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Shaghayegh Habibi
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Avneesh Gautam
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - F. Keerti
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Caihong Bi
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
| | - Tianshu Xiao
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yongfei Cai
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Bing Chen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Duane R. Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Ragon Institute of MGH, MIT, and Harvard
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20
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Lu X, Yamasaki S. Current understanding of T cell immunity against SARS-CoV-2. Inflamm Regen 2022; 42:51. [PMID: 36447270 PMCID: PMC9706904 DOI: 10.1186/s41232-022-00242-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
As an important part of adaptive immunity, T cells are indispensable in the defense against pathogens including viruses. SARS-CoV-2 is a new human coronavirus that occurred at the end of 2019 and has caused the COVID-19 pandemic. Nevertheless, most of the infected patients recovered without any antiviral therapies, suggesting an effective immunity developed in the bodies. T cell immunity responds upon SARS-CoV-2 infection or vaccination and plays crucial roles in eliminating the viruses and generating T cell memory. Specifically, a subpopulation of CD4+ T cells could support the production of anti-SARS-CoV-2 antibodies, and cytotoxic CD8+ T cells are also protective against the infection. SARS-CoV-2-recognizing T cells could be detected in SARS-CoV-2-unexposed donors, but the role of these cross-reactive T cells is still in debate. T cell responses could be diverse across individuals, mainly due to the polymorphism of HLAs. Thus, compared to antibodies, T cell responses are generally less affected by the mutations of SARS-CoV-2 variants. Up to now, a huge number of studies on SARS-CoV-2-responsive T cells have been published. In this review, we introduced some major findings addressing the questions in the main aspects about T cell responses elicited by SARS-CoV-2, to summarize the current understanding of COVID-19.
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Affiliation(s)
- Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871 Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
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21
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Lima K, Fontoura JC, de Souza PO, Fazolo T, Hilario G, Zorzetto R, Rodrigues Junior LC, Coimbra LD, Borin A, Bispo-dos-Santos K, Granja F, Marques RE, Zavaglia GO, Fernandes IR, Varela FH, Polese-Bonatto M, Tonini ML, Ikeda do Carmo GM, de Almeida WAF, Borges TJ, Nakaya HI, Proenca-Modena JL, Callegari-Jacques SM, Scotta MC, Stein RT, Bonorino C. SARS-CoV-2 infected children form early immune memory responses dominated by nucleocapsid-specific CD8+ T cells and antibodies. Front Immunol 2022; 13:1033364. [PMID: 36405692 PMCID: PMC9667737 DOI: 10.3389/fimmu.2022.1033364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/03/2022] [Indexed: 08/13/2023] Open
Abstract
This is the third year of the SARS-CoV-2 pandemic, and yet most children remain unvaccinated. COVID-19 in children manifests as mostly mild or asymptomatic, however high viral titers and strong cellular and humoral responses are observed upon acute infection. It is still unclear how long these responses persist, and if they can protect from re-infection and/or disease severity. Here, we analyzed immune memory responses in a cohort of children and adults with COVID-19. Important differences between children and adults are evident in kinetics and profile of memory responses. Children develop early N-specific cytotoxic T cell responses, that rapidly expand and dominate their immune memory to the virus. Children's anti-N, but not anti-S, antibody titers increase over time. Neutralization titers correlate with N-specific antibodies and CD8+T cells. However, antibodies generated by infection do not efficiently cross-neutralize variants Gamma or Delta. Our results indicate that mechanisms that protect from disease severity are possibly different from those that protect from reinfection, bringing novel insights for pediatric vaccine design. They also underline the importance of vaccination in children, who remain at risk for COVID-19 despite having been previously infected.
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Affiliation(s)
- Karina Lima
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Julia C. Fontoura
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Priscila Oliveira de Souza
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Tiago Fazolo
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Gabriel Hilario
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Renata Zorzetto
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Luiz C Rodrigues Junior
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
| | - Lais D. Coimbra
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre Borin
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Karina Bispo-dos-Santos
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
- Biodiversity Research Centre, Federal University of Roraima (UFRR), Boa Vista, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriela Oliveira Zavaglia
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Ingrid Rodrigues Fernandes
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Fernanda Hammes Varela
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Marcia Polese-Bonatto
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Maiko Luís Tonini
- Coordenação-Geral de Vigilância das Doenças de Transmissão Respiratória de Condições Crônicas, Departamento de Doenças de Condições Crônicas e IST, Secretaria de Vigilância em Saúde – Ministério da Saúde (CGDR/DCCI/SVS/MS)., Brasília, Brazil
| | - Greice Madeleine Ikeda do Carmo
- Departamento de Imunizações e doenças transmissíveis, Secretaria de Vigilância em Saúde - Ministério da Saúde (DEIDT/SVS/MS), Brasília, Brazil
| | | | - Thiago J. Borges
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Helder I. Nakaya
- Computational System Biology Laboratory (CSBL), Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
- Hub of Global Health (HGH), University of Campinas (Unicamp), Campinas, Brazil
| | | | - Marcelo Comerlato Scotta
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
- Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul – PUCRS, Porto Alegre, Brazil
| | - Renato T. Stein
- Social Responsibility – Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI-SUS ), Hospital Moinhos de Vento, Porto Alegre, Brazil
- Escola de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul – PUCRS, Porto Alegre, Brazil
| | - Cristina Bonorino
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA, Porto Alegre, Brazil
- Department of Surgery, University of California at San Diego – UCSD, La Jolla, CA, United States
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22
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Diani S, Leonardi E, Cavezzi A, Ferrari S, Iacono O, Limoli A, Bouslenko Z, Natalini D, Conti S, Mantovani M, Tramonte S, Donzelli A, Serravalle E. SARS-CoV-2-The Role of Natural Immunity: A Narrative Review. J Clin Med 2022; 11:6272. [PMID: 36362500 PMCID: PMC9655392 DOI: 10.3390/jcm11216272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Both natural immunity and vaccine-induced immunity to COVID-19 may be useful to reduce the mortality/morbidity of this disease, but still a lot of controversy exists. AIMS This narrative review analyzes the literature regarding these two immunitary processes and more specifically: (a) the duration of natural immunity; (b) cellular immunity; (c) cross-reactivity; (d) the duration of post-vaccination immune protection; (e) the probability of reinfection and its clinical manifestations in the recovered patients; (f) the comparisons between vaccinated and unvaccinated as to the possible reinfections; (g) the role of hybrid immunity; (h) the effectiveness of natural and vaccine-induced immunity against Omicron variant; (i) the comparative incidence of adverse effects after vaccination in recovered individuals vs. COVID-19-naïve subjects. MATERIAL AND METHODS through multiple search engines we investigated COVID-19 literature related to the aims of the review, published since April 2020 through July 2022, including also the previous articles pertinent to the investigated topics. RESULTS nearly 900 studies were collected, and 246 pertinent articles were included. It was highlighted that the vast majority of the individuals after suffering from COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality. CONCLUSIONS this extensive narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Consequently, vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: (a) measure the durability of immunity over time; (b) evaluate both the impacts of Omicron BA.5 on vaccinated and healed subjects and the role of hybrid immunity.
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Affiliation(s)
- Sara Diani
- School of Musictherapy, Université Européenne Jean Monnet, 35129 Padova, Italy
| | | | | | | | - Oriana Iacono
- Physical Medicine and Rehabilitation Department, Mirandola Hospital, 41037 Mirandola, Italy
| | - Alice Limoli
- ARPAV (Regional Agency for the Environment Protection), 31100 Treviso, Italy
| | - Zoe Bouslenko
- Cardiology Department, Valdese Hospital, 10100 Torino, Italy
| | | | | | | | - Silvano Tramonte
- Environment and Health Commission, National Bioarchitecture Institute, 20121 Milano, Italy
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23
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Stolfi P, Castiglione F, Mastrostefano E, Di Biase I, Di Biase S, Palmieri G, Prisco A. In-silico evaluation of adenoviral COVID-19 vaccination protocols: Assessment of immunological memory up to 6 months after the third dose. Front Immunol 2022; 13:998262. [PMID: 36353634 PMCID: PMC9639861 DOI: 10.3389/fimmu.2022.998262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background The immune response to adenoviral COVID-19 vaccines is affected by the interval between doses. The optimal interval is unknown. Aim We aim to explore in-silico the effect of the interval between vaccine administrations on immunogenicity and to analyze the contribution of pre-existing levels of antibodies, plasma cells, and memory B and T lymphocytes. Methods We used a stochastic agent-based immune simulation platform to simulate two-dose and three-dose vaccination protocols with an adenoviral vaccine. We identified the model’s parameters fitting anti-Spike antibody levels from individuals immunized with the COVID-19 vaccine AstraZeneca (ChAdOx1-S, Vaxzevria). We used several statistical methods, such as principal component analysis and binary classification, to analyze the correlation between pre-existing levels of antibodies, plasma cells, and memory B and T cells to the magnitude of the antibody response following a booster dose. Results and conclusions We find that the magnitude of the antibody response to a booster depends on the number of pre-existing memory B cells, which, in turn, is highly correlated to the number of T helper cells and plasma cells, and the antibody titers. Pre-existing memory T cytotoxic cells and antibodies directly influence antigen availability hence limiting the magnitude of the immune response. The optimal immunogenicity of the third dose is achieved over a large time window, spanning from 6 to 16 months after the second dose. Interestingly, after any vaccine dose, individuals can be classified into two groups, sustainers and decayers, that differ in the kinetics of decline of their antibody titers due to differences in long-lived plasma cells. This suggests that the decayers may benefit from a tailored boosting schedule with a shorter interval to avoid the temporary loss of serological immunity.
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Affiliation(s)
- Paola Stolfi
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy
| | - Enrico Mastrostefano
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy
- *Correspondence: Enrico Mastrostefano, ; Antonella Prisco,
| | | | | | - Gianna Palmieri
- Institute of Biosciences and BioResources, National Research Council, Naples, Italy
| | - Antonella Prisco
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- *Correspondence: Enrico Mastrostefano, ; Antonella Prisco,
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Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. RESEARCH SQUARE 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
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25
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Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB. A novel vaccine based on SARS-CoV-2 CD4 + and CD8 + T cell conserved epitopes from variants Alpha to Omicron. Sci Rep 2022; 12:16731. [PMID: 36202985 PMCID: PMC9537284 DOI: 10.1038/s41598-022-21207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/23/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 caused, as of September, 1rst, 2022, 599,825,400 confirmed cases, including 6,469,458 deaths. Currently used vaccines reduced severity and mortality but not virus transmission or reinfection by different strains. They are based on the Spike protein of the Wuhan reference virus, which although highly antigenic suffered many mutations in SARS-CoV-2 variants, escaping vaccine-generated immune responses. Multiepitope vaccines based on 100% conserved epitopes of multiple proteins of all SARS-CoV-2 variants, rather than a single highly mutating antigen, could offer more long-lasting protection. In this study, a multiepitope multivariant vaccine was designed using immunoinformatics and in silico approaches. It is composed of highly promiscuous and strong HLA binding CD4+ and CD8+ T cell epitopes of the S, M, N, E, ORF1ab, ORF 6 and ORF8 proteins. Based on the analysis of one genome per WHO clade, the epitopes were 100% conserved among the Wuhan-Hu1, Alpha, Beta, Gamma, Delta, Omicron, Mµ, Zeta, Lambda and R1 variants. An extended epitope-conservancy analysis performed using GISAID metadata of 3,630,666 SARS-CoV-2 genomes of these variants and the additional genomes of the Epsilon, Lota, Theta, Eta, Kappa and GH490 R clades, confirmed the high conservancy of the epitopes. All but one of the CD4 peptides showed a level of conservation greater than 97% among all genomes. All but one of the CD8 epitopes showed a level of conservation greater than 96% among all genomes, with the vast majority greater than 99%. A multiepitope and multivariant recombinant vaccine was designed and it was stable, mildly hydrophobic and non-toxic. The vaccine has good molecular docking with TLR4 and promoted, without adjuvant, strong B and Th1 memory immune responses and secretion of high levels of IL-2, IFN-γ, lower levels of IL-12, TGF-β and IL-10, and no IL-6. Experimental in vivo studies should validate the vaccine’s further use as preventive tool with cross-protective properties.
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Affiliation(s)
- Iam Palatnik-de-Sousa
- Department of Electrical Engeneering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stephany Christiny Cavalcante
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Paula Fonseca Ribeiro
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Antônio Barbosa Martins Silva
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ciro Cavalcante
- Department of Pharmacy, Campus Professor Antônio Garcia Filho, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Global Virus Network, Baltimore, MD, USA
| | - Clarisa Beatriz Palatnik-de-Sousa
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. .,Institute for Immunological Investigation (III), INCT, National Council for Scientific and Technological Development (CNPq), São Paulo, Brazil.
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