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Olawade DB, Teke J, Fapohunda O, Weerasinghe K, Usman SO, Ige AO, Clement David-Olawade A. Leveraging artificial intelligence in vaccine development: A narrative review. J Microbiol Methods 2024; 224:106998. [PMID: 39019262 DOI: 10.1016/j.mimet.2024.106998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Vaccine development stands as a cornerstone of public health efforts, pivotal in curbing infectious diseases and reducing global morbidity and mortality. However, traditional vaccine development methods are often time-consuming, costly, and inefficient. The advent of artificial intelligence (AI) has ushered in a new era in vaccine design, offering unprecedented opportunities to expedite the process. This narrative review explores the role of AI in vaccine development, focusing on antigen selection, epitope prediction, adjuvant identification, and optimization strategies. AI algorithms, including machine learning and deep learning, leverage genomic data, protein structures, and immune system interactions to predict antigenic epitopes, assess immunogenicity, and prioritize antigens for experimentation. Furthermore, AI-driven approaches facilitate the rational design of immunogens and the identification of novel adjuvant candidates with optimal safety and efficacy profiles. Challenges such as data heterogeneity, model interpretability, and regulatory considerations must be addressed to realize the full potential of AI in vaccine development. Integrating emerging technologies, such as single-cell omics and synthetic biology, promises to enhance vaccine design precision and scalability. This review underscores the transformative impact of AI on vaccine development and highlights the need for interdisciplinary collaborations and regulatory harmonization to accelerate the delivery of safe and effective vaccines against infectious diseases.
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Affiliation(s)
- David B Olawade
- Department of Allied and Public Health, School of Health, Sport and Bioscience, University of East London, London, United Kingdom; Department of Research and Innovation, Medway NHS Foundation Trust, Gillingham ME7 5NY, United Kingdom.
| | - Jennifer Teke
- Department of Research and Innovation, Medway NHS Foundation Trust, Gillingham ME7 5NY, United Kingdom; Faculty of Medicine, Health and Social Care, Canterbury Christ Church University, United Kingdom
| | | | - Kusal Weerasinghe
- Department of Research and Innovation, Medway NHS Foundation Trust, Gillingham ME7 5NY, United Kingdom
| | - Sunday O Usman
- Department of Systems and Industrial Engineering, University of Arizona, USA
| | - Abimbola O Ige
- Department of Chemistry, Faculty of Science, University of Ibadan, Ibadan, Nigeria
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Braun A, Rowntree LC, Huang Z, Pandey K, Thuesen N, Li C, Petersen J, Littler DR, Raji S, Nguyen THO, Jappe Lange E, Persson G, Schantz Klausen M, Kringelum J, Chung S, Croft NP, Faridi P, Ayala R, Rossjohn J, Illing PT, Scull KE, Ramarathinam S, Mifsud NA, Kedzierska K, Sørensen AB, Purcell AW. Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes. Nat Commun 2024; 15:7547. [PMID: 39214998 PMCID: PMC11364864 DOI: 10.1038/s41467-024-51959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Most COVID-19 vaccines elicit immunity against the SARS-CoV-2 Spike protein. However, Spike protein mutations in emerging strains and immune evasion by the SARS-CoV-2 virus demonstrates the need to develop more broadly targeting vaccines. To facilitate this, we use mass spectrometry to identify immunopeptides derived from seven relatively conserved structural and non-structural SARS-CoV-2 proteins (N, E, Nsp1/4/5/8/9). We use two different B-lymphoblastoid cell lines to map Human Leukocyte Antigen (HLA) class I and class II immunopeptidomes covering some of the prevalent HLA types across the global human population. We employ DNA plasmid transfection and direct antigen delivery approaches to sample different antigens and find 248 unique HLA class I and HLA class II bound peptides with 71 derived from N, 12 from E, 28 from Nsp1, 19 from Nsp4, 73 from Nsp8 and 45 peptides derived from Nsp9. Over half of the viral peptides are unpublished. T cell reactivity tested against 56 of the detected peptides shows CD8+ and CD4+ T cell responses against several peptides from the N, E, and Nsp9 proteins. Results from this study will aid the development of next-generation COVID vaccines targeting epitopes from across a number of SARS-CoV-2 proteins.
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Affiliation(s)
- Asolina Braun
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ziyi Huang
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | | | - Chen Li
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jan Petersen
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Dene R Littler
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Shabana Raji
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | | | | | | | - Shanzou Chung
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, UK
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine E Scull
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sri Ramarathinam
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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Ehrlich R, Glynn E, Singh M, Ghersi D. Computational Methods for Predicting Key Interactions in T Cell-Mediated Adaptive Immunity. Annu Rev Biomed Data Sci 2024; 7:295-316. [PMID: 38748864 DOI: 10.1146/annurev-biodatasci-102423-122741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024]
Abstract
The adaptive immune system recognizes pathogen- and cancer-specific features and is endowed with memory, enabling it to respond quickly and efficiently to repeated encounters with the same antigens. T cells play a central role in the adaptive immune system by directly targeting intracellular pathogens and helping to activate B cells to secrete antibodies. Several fundamental protein interactions-including those between major histocompatibility complex (MHC) proteins and antigen-derived peptides as well as between T cell receptors and peptide-MHC complexes-underlie the ability of T cells to recognize antigens with great precision. Computational approaches to predict these interactions are increasingly being used for medically relevant applications, including vaccine design and prediction of patient response to cancer immunotherapies. We provide computational researchers with an accessible introduction to the adaptive immune system, review computational approaches to predict the key protein interactions underlying T cell-mediated adaptive immunity, and highlight remaining challenges.
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Affiliation(s)
- Ryan Ehrlich
- School of Interdisciplinary Informatics, University of Nebraska, Omaha, Nebraska, USA;
| | - Eric Glynn
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, USA
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA;
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, USA
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska, Omaha, Nebraska, USA;
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Lischer C, Eberhardt M, Flamann C, Berges J, Güse E, Wessely A, Weich A, Retzlaff J, Dörrie J, Schaft N, Wiesinger M, März J, Schuler-Thurner B, Knorr H, Gupta S, Singh KP, Schuler G, Heppt MV, Koch EAT, van Kleef ND, Freen-van Heeren JJ, Turksma AW, Wolkenhauer O, Hohberger B, Berking C, Bruns H, Vera J. Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy. J Immunother Cancer 2024; 12:e008104. [PMID: 38724462 PMCID: PMC11086525 DOI: 10.1136/jitc-2023-008104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.
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Affiliation(s)
- Christopher Lischer
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Martin Eberhardt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Cindy Flamann
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Berges
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Esther Güse
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Anja Wessely
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Adrian Weich
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jimmy Retzlaff
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jan Dörrie
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niels Schaft
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Manuel Wiesinger
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Johannes März
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Beatrice Schuler-Thurner
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Harald Knorr
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Krishna Pal Singh
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Gerold Schuler
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus Vincent Heppt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Elias Andreas Thomas Koch
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Bettina Hohberger
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Carola Berking
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Heiko Bruns
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
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Fathollahi M, Motamedi H, Hossainpour H, Abiri R, Shahlaei M, Moradi S, Dashtbin S, Moradi J, Alvandi A. Designing a novel multi-epitopes pan-vaccine against SARS-CoV-2 and seasonal influenza: in silico and immunoinformatics approach. J Biomol Struct Dyn 2023:1-24. [PMID: 37723861 DOI: 10.1080/07391102.2023.2258420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
Abstract
The merger of COVID-19 and seasonal influenza infections is considered a potentially serious threat to public health. These two viral agents can cause extensive and severe lower and upper respiratory tract infections with lung damage with host factors. Today, the development of vaccination has been shown to reduce the risk of hospitalization and mortality from the COVID-19 virus and influenza epidemics. Therefore, this study contributes to an immunoinformatics approach to producing a vaccine that can elicit strong and specific immune responses against COVID-19 and influenza A and B viruses. The NCBI, GISAID, and Uniprot databases were used to retrieve sequences. Linear B cell, Cytotoxic T lymphocyte, and Helper T lymphocyte epitopes were predicted using the online servers. Population coverage of MHC I epitopes worldwide for SARS-CoV-2, Influenza virus H3N2, H3N2, and Yamagata/Victoria were 99.93%, 68.67%, 68.38%, and 85.45%, respectively. Candidate epitopes were linked by GGGGS, GPGPG, and KK linkers. Different epitopes were permutated several times to form different peptides and then screened for antigenicity, allergenicity, and toxicity. The vaccine construct was analyzed for physicochemical properties, conformational B-cell epitopes, interaction with Toll-like receptors, and IFN-gamma-induced. Immune stimulation response of final construct was evaluated using C-IMMSIM. Eventually, the final construct sequence was codon-optimized for Escherichia coli K12 and Homo sapiens to design a multi-epitope vaccine and mRNA vaccine. In conclusion, due to the variable nature of SARS-CoV-2 and influenza proteins, the design of a multi-epitope vaccine can protect against all their standard variants, but laboratory validation is required.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Matin Fathollahi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid Motamedi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hadi Hossainpour
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shirin Dashtbin
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jale Moradi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
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6
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Lie-Andersen O, Hübbe ML, Subramaniam K, Steen-Jensen D, Bergmann AC, Justesen D, Holmström MO, Turtle L, Justesen S, Lança T, Hansen M. Impact of peptide:HLA complex stability for the identification of SARS-CoV-2-specific CD8 +T cells. Front Immunol 2023; 14:1151659. [PMID: 37275886 PMCID: PMC10232890 DOI: 10.3389/fimmu.2023.1151659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Induction of a lasting protective immune response is dependent on presentation of epitopes to patrolling T cells through the HLA complex. While peptide:HLA (pHLA) complex affinity alone is widely exploited for epitope selection, we demonstrate that including the pHLA complex stability as a selection parameter can significantly reduce the high false discovery rate observed with predicted affinity. In this study, pHLA complex stability was measured on three common class I alleles and 1286 overlapping 9-mer peptides derived from the SARS-CoV-2 Spike protein. Peptides were pooled based on measured stability and predicted affinity. Strikingly, stability of the pHLA complex was shown to strongly select for immunogenic epitopes able to activate functional CD8+T cells. This result was observed across the three studied alleles and in both vaccinated and convalescent COVID-19 donors. Deconvolution of peptide pools showed that specific CD8+T cells recognized one or two dominant epitopes. Moreover, SARS-CoV-2 specific CD8+T cells were detected by tetramer-staining across multiple donors. In conclusion, we show that stability analysis of pHLA is a key factor for identifying immunogenic epitopes.
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Affiliation(s)
- Olivia Lie-Andersen
- Immunitrack ApS, Copenhagen, Denmark
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Mie Linder Hübbe
- Immunitrack ApS, Copenhagen, Denmark
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Krishanthi Subramaniam
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Morten Orebo Holmström
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Morten Hansen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
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Gao F, Mallajosyula V, Arunachalam PS, van der Ploeg K, Manohar M, Röltgen K, Yang F, Wirz O, Hoh R, Haraguchi E, Lee JY, Willis R, Ramachandiran V, Li J, Kathuria KR, Li C, Lee AS, Shah MM, Sindher SB, Gonzalez J, Altman JD, Wang TT, Boyd SD, Pulendran B, Jagannathan P, Nadeau KC, Davis MM. Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8 + T cell responses post SARS-CoV-2 infection. Immunity 2023; 56:864-878.e4. [PMID: 36996809 PMCID: PMC10017386 DOI: 10.1016/j.immuni.2023.03.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/05/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
T cells are a critical component of the response to SARS-CoV-2, but their kinetics after infection and vaccination are insufficiently understood. Using "spheromer" peptide-MHC multimer reagents, we analyzed healthy subjects receiving two doses of the Pfizer/BioNTech BNT162b2 vaccine. Vaccination resulted in robust spike-specific T cell responses for the dominant CD4+ (HLA-DRB1∗15:01/S191) and CD8+ (HLA-A∗02/S691) T cell epitopes. Antigen-specific CD4+ and CD8+ T cell responses were asynchronous, with the peak CD4+ T cell responses occurring 1 week post the second vaccination (boost), whereas CD8+ T cells peaked 2 weeks later. These peripheral T cell responses were elevated compared with COVID-19 patients. We also found that previous SARS-CoV-2 infection resulted in decreased CD8+ T cell activation and expansion, suggesting that previous infection can influence the T cell response to vaccination.
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Affiliation(s)
- Fei Gao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Kattria van der Ploeg
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ramona Hoh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily Haraguchi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard Willis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Jiefu Li
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Karan Raj Kathuria
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra S Lee
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mihir M Shah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Gonzalez
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John D Altman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard, MA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
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Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
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9
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Fuertes MA, Alonso C. New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome. Curr Genomics 2023; 23:424-440. [PMID: 37920558 PMCID: PMC10173420 DOI: 10.2174/1389202924666230202152351] [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: 04/27/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Methods A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other. Results We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions. Conclusion Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
| | - Carlos Alonso
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
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10
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Vijver SV, Danklmaier S, Pipperger L, Gronauer R, Floriani G, Hackl H, Das K, Wollmann G. Prediction and validation of murine MHC class I epitopes of the recombinant virus VSV-GP. Front Immunol 2023; 13:1100730. [PMID: 36741416 PMCID: PMC9893851 DOI: 10.3389/fimmu.2022.1100730] [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: 11/17/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Oncolytic viruses are currently tested as a novel platform for cancer therapy. These viruses preferentially replicate in and kill malignant cells. Due to their microbial origin, treatment with oncolytic viruses naturally results in anti-viral responses and general immune activation. Consequently, the oncolytic virus treatment also induces anti-viral T cells. Since these can constitute the dominant activated T cell pool, monitoring of the anti-viral T cell response may aid in better understanding of the immune responses post oncolytic virotherapy. This study aimed to identify the anti-viral T cells raised by VSV-GP virotherapy in C57BL/6J mice, one of the most widely used models for preclinical studies. VSV-GP is a novel oncolytic agent that recently entered a clinical phase I study. To identify the VSV-GP epitopes to which mouse anti-viral T cells react, we used a multilevel adapted bioinformatics viral epitope prediction approach based on the tools netMHCpan, MHCflurry and netMHCstabPan, which are commonly used in neoepitope identification. Predicted viral epitopes were ranked based on consensus binding strength categories, predicted stability, and dissimilarity to the mouse proteome. The top ranked epitopes were selected and included in the peptide candidate matrix in order to use a matrix deconvolution approach. Using ELISpot, we showed which viral epitopes presented on C57BL/6J mouse MHC-I alleles H2-Db and H2-Kb trigger IFN-γ secretion due to T cell activation. Furthermore, we validated these findings using an intracellular cytokine staining. Collectively, identification of the VSV-GP T cell epitopes enables monitoring of the full range of anti-viral T cell responses upon VSV-GP virotherapy in future studies with preclinical mouse models to more comprehensively delineate anti-viral from anti-tumor T cell responses. These findings also support the development of novel VSV-GP variants expressing immunomodulatory transgenes and can improve the assessment of anti-viral immunity in preclinical models.
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Affiliation(s)
- Saskia V. Vijver
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Sarah Danklmaier
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Pipperger
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
| | - Raphael Gronauer
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriel Floriani
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Guido Wollmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Viral Immunotherapy of Cancer, Medical University of Innsbruck, Innsbruck, Austria
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11
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Sei S, Ahadova A, Keskin DB, Bohaumilitzky L, Gebert J, von Knebel Doeberitz M, Lipkin SM, Kloor M. Lynch syndrome cancer vaccines: A roadmap for the development of precision immunoprevention strategies. Front Oncol 2023; 13:1147590. [PMID: 37035178 PMCID: PMC10073468 DOI: 10.3389/fonc.2023.1147590] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Hereditary cancer syndromes (HCS) account for 5~10% of all cancer diagnosis. Lynch syndrome (LS) is one of the most common HCS, caused by germline mutations in the DNA mismatch repair (MMR) genes. Even with prospective cancer surveillance, LS is associated with up to 50% lifetime risk of colorectal, endometrial, and other cancers. While significant progress has been made in the timely identification of germline pathogenic variant carriers and monitoring and early detection of precancerous lesions, cancer-risk reduction strategies are still centered around endoscopic or surgical removal of neoplastic lesions and susceptible organs. Safe and effective cancer prevention strategies are critically needed to improve the life quality and longevity of LS and other HCS carriers. The era of precision oncology driven by recent technological advances in tumor molecular profiling and a better understanding of genetic risk factors has transformed cancer prevention approaches for at-risk individuals, including LS carriers. MMR deficiency leads to the accumulation of insertion and deletion mutations in microsatellites (MS), which are particularly prone to DNA polymerase slippage during DNA replication. Mutations in coding MS give rise to frameshift peptides (FSP) that are recognized by the immune system as neoantigens. Due to clonal evolution, LS tumors share a set of recurrent and predictable FSP neoantigens in the same and in different LS patients. Cancer vaccines composed of commonly recurring FSP neoantigens selected through prediction algorithms have been clinically evaluated in LS carriers and proven safe and immunogenic. Preclinically analogous FSP vaccines have been shown to elicit FSP-directed immune responses and exert tumor-preventive efficacy in murine models of LS. While the immunopreventive efficacy of "off-the-shelf" vaccines consisting of commonly recurring FSP antigens is currently investigated in LS clinical trials, the feasibility and utility of personalized FSP vaccines with individual HLA-restricted epitopes are being explored for more precise targeting. Here, we discuss recent advances in precision cancer immunoprevention approaches, emerging enabling technologies, research gaps, and implementation barriers toward clinical translation of risk-tailored prevention strategies for LS carriers. We will also discuss the feasibility and practicality of next-generation cancer vaccines that are based on personalized immunogenic epitopes for precision cancer immunoprevention.
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Affiliation(s)
- Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Derin B. Keskin
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of The Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Lena Bohaumilitzky
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Steven M. Lipkin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, United States
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- *Correspondence: Shizuko Sei, ; Steven M. Lipkin, ; Matthias Kloor,
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12
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Ji XS, Chen B, Ze B, Zhou WH. Human genetic basis of severe or critical illness in COVID-19. Front Cell Infect Microbiol 2022; 12:963239. [PMID: 36204639 PMCID: PMC9530247 DOI: 10.3389/fcimb.2022.963239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to considerable morbidity and mortality worldwide. The clinical manifestation of COVID-19 ranges from asymptomatic or mild infection to severe or critical illness, such as respiratory failure, multi-organ dysfunction or even death. Large-scale genetic association studies have indicated that genetic variations affecting SARS-CoV-2 receptors (angiotensin-converting enzymes, transmembrane serine protease-2) and immune components (Interferons, Interleukins, Toll-like receptors and Human leukocyte antigen) are critical host determinants related to the severity of COVID-19. Genetic background, such as 3p21.31 and 9q34.2 loci were also identified to influence outcomes of COVID-19. In this review, we aimed to summarize the current literature focusing on human genetic factors that may contribute to the observed diversified severity of COVID-19. Enhanced understanding of host genetic factors and viral interactions of SARS-CoV-2 could provide scientific bases for personalized preventive measures and precision medicine strategies.
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Affiliation(s)
- Xiao-Shan Ji
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bin Chen
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bi Ze
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wen-Hao Zhou
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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13
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Agarwal A, Beck KL, Capponi S, Kunitomi M, Nayar G, Seabolt E, Mahadeshwar G, Bianco S, Mukherjee V, Kaufman JH. Predicting Epitope Candidates for SARS-CoV-2. Viruses 2022; 14:1837. [PMID: 36016459 PMCID: PMC9416013 DOI: 10.3390/v14081837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known epitope sequences from SARS-CoV, SARS-CoV-2, and other Coronaviridae were leveraged to identify additional antigen regions in 62K SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, and discuss where epitopes are located on proteins and how epitopes can be grouped into classes. The mutation density of different protein regions is presented using a big data approach. It was observed that there are 112 B cell and 279 T cell conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike glycoprotein.
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Affiliation(s)
- Akshay Agarwal
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Kristen L. Beck
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Sara Capponi
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- NSF Center for Cellular Construction, San Francisco, CA 94158, USA
| | - Mark Kunitomi
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Gowri Nayar
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Edward Seabolt
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Gandhar Mahadeshwar
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- NSF Center for Cellular Construction, San Francisco, CA 94158, USA
| | - Vandana Mukherjee
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - James H. Kaufman
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
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14
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Sharma A, Virmani T, Pathak V, Sharma A, Pathak K, Kumar G, Pathak D. Artificial Intelligence-Based Data-Driven Strategy to Accelerate Research, Development, and Clinical Trials of COVID Vaccine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7205241. [PMID: 35845955 PMCID: PMC9279074 DOI: 10.1155/2022/7205241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5-15 years to 1-2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
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Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Vipluv Pathak
- GL Bajaj Institute of Technology and Management, Greater Noida, Uttar Pradesh, India
| | | | - Kamla Pathak
- Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh 206001, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Devender Pathak
- Rajiv Academy for Pharmacy, NH. #2, Mathura Delhi Road P.O, Chhatikara, Mathura, Uttar Pradesh 281001, India
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15
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Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022; 1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy.
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Affiliation(s)
- Kyle R Jackson
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ariana R Maleki
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kano Amagai
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Avery Salmon
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun S Katailiha
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Romanos Fasoulis
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Brenda D Melendez
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | - Yang Liu
- ThermoFisher Scientific, San Jose, CA, USA
| | - David Horn
- ThermoFisher Scientific, San Jose, CA, USA
| | | | | | - Patrick Hwu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Gregory Lizée
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
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16
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Abstract
This review discusses peptide epitopes used as antigens in the development of vaccines in clinical trials as well as future vaccine candidates. It covers peptides used in potential immunotherapies for infectious diseases including SARS-CoV-2, influenza, hepatitis B and C, HIV, malaria, and others. In addition, peptides for cancer vaccines that target examples of overexpressed proteins are summarized, including human epidermal growth factor receptor 2 (HER-2), mucin 1 (MUC1), folate receptor, and others. The uses of peptides to target cancers caused by infective agents, for example, cervical cancer caused by human papilloma virus (HPV), are also discussed. This review also provides an overview of model peptide epitopes used to stimulate non-specific immune responses, and of self-adjuvanting peptides, as well as the influence of other adjuvants on peptide formulations. As highlighted in this review, several peptide immunotherapies are in advanced clinical trials as vaccines, and there is great potential for future therapies due the specificity of the response that can be achieved using peptide epitopes.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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17
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Gustiananda M, Sulistyo BP, Agustriawan D, Andarini S. Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population. Vaccines (Basel) 2021; 9:1459. [PMID: 34960205 PMCID: PMC8704007 DOI: 10.3390/vaccines9121459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon's entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia.
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Affiliation(s)
- Marsia Gustiananda
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - Bobby Prabowo Sulistyo
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - David Agustriawan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia;
| | - Sita Andarini
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine University of Indonesia, Persahabatan Hospital, Jl Persahabatan Raya 1, Jakarta 13230, Indonesia;
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18
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Jin X, Ding Y, Sun S, Wang X, Zhou Z, Liu X, Li M, Chen X, Shen A, Wu Y, Liu B, Zhang J, Li J, Yang Y, Qiu H, Shen C, He Y, Zhao G. Screening HLA-A-restricted T cell epitopes of SARS-CoV-2 and the induction of CD8 + T cell responses in HLA-A transgenic mice. Cell Mol Immunol 2021; 18:2588-2608. [PMID: 34728796 PMCID: PMC8561351 DOI: 10.1038/s41423-021-00784-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific T cells have been found to play essential roles in host immune protection and pathology in patients with coronavirus disease 2019 (COVID-19), this study focused on the functional validation of T cell epitopes and the development of vaccines that induce specific T cell responses. A total of 120 CD8+ T cell epitopes from the E, M, N, S, and RdRp proteins were functionally validated. Among these, 110, 15, 6, 14, and 12 epitopes were highly homologous with SARS-CoV, OC43, NL63, HKU1, and 229E, respectively; in addition, four epitopes from the S protein displayed one amino acid that was distinct from the current SARS-CoV-2 variants. Then, 31 epitopes restricted by the HLA-A2 molecule were used to generate peptide cocktail vaccines in combination with Poly(I:C), R848 or poly (lactic-co-glycolic acid) nanoparticles, and these vaccines elicited robust and specific CD8+ T cell responses in HLA-A2/DR1 transgenic mice as well as wild-type mice. In contrast to previous research, this study established a modified DC-peptide-PBL cell coculture system using healthy donor PBMCs to validate the in silico predicted epitopes, provided an epitope library restricted by nine of the most prevalent HLA-A allotypes covering broad Asian populations, and identified the HLA-A restrictions of these validated epitopes using competitive peptide binding experiments with HMy2.CIR cell lines expressing the indicated HLA-A allotype, which initially confirmed the in vivo feasibility of 9- or 10-mer peptide cocktail vaccines against SARS-CoV-2. These data will facilitate the design and development of vaccines that induce antiviral CD8+ T cell responses in COVID-19 patients.
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Affiliation(s)
- Xiaoxiao Jin
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yan Ding
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xinyi Wang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zining Zhou
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Miaomiao Li
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Xian Chen
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Anran Shen
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Bicheng Liu
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jianqiong Zhang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jian Li
- Life Science & Technology School of Southeast University, Nanjing, 210096, Jiangsu, China
| | - Yi Yang
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Haibo Qiu
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Yuxian He
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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19
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Ferreira CS, Martins YC, Souza RC, Vasconcelos ATR. EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes. PeerJ 2021; 9:e12548. [PMID: 34909278 PMCID: PMC8641484 DOI: 10.7717/peerj.12548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.
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Affiliation(s)
- Cristina S. Ferreira
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Yasmmin C. Martins
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Rangel Celso Souza
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Ana Tereza R. Vasconcelos
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
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20
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Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Brief Bioinform 2021; 22:bbab160. [PMID: 34009266 PMCID: PMC8135853 DOI: 10.1093/bib/bbab160] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Cytolytic T-cells play an essential role in the adaptive immune system by seeking out, binding and killing cells that present foreign antigens on their surface. An improved understanding of T-cell immunity will greatly aid in the development of new cancer immunotherapies and vaccines for life-threatening pathogens. Central to the design of such targeted therapies are computational methods to predict non-native peptides to elicit a T-cell response, however, we currently lack accurate immunogenicity inference methods. Another challenge is the ability to accurately simulate immunogenic peptides for specific human leukocyte antigen alleles, for both synthetic biological applications, and to augment real training datasets. Here, we propose a beta-binomial distribution approach to derive peptide immunogenic potential from sequence alone. We conducted systematic benchmarking of five traditional machine learning (ElasticNet, K-nearest neighbors, support vector machine, Random Forest and AdaBoost) and three deep learning models (convolutional neural network (CNN), Residual Net and graph neural network) using three independent prior validated immunogenic peptide collections (dengue virus, cancer neoantigen and SARS-CoV-2). We chose the CNN as the best prediction model, based on its adaptivity for small and large datasets and performance relative to existing methods. In addition to outperforming two highly used immunogenicity prediction algorithms, DeepImmuno-CNN correctly predicts which residues are most important for T-cell antigen recognition and predicts novel impacts of SARS-CoV-2 variants. Our independent generative adversarial network (GAN) approach, DeepImmuno-GAN, was further able to accurately simulate immunogenic peptides with physicochemical properties and immunogenicity predictions similar to that of real antigens. We provide DeepImmuno-CNN as source code and an easy-to-use web interface.
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Affiliation(s)
- Guangyuan Li
- University of Cincinnati, 3333 Burnet Ave, MLC7024, Cincinnati, OH 45267, USA
| | | | - V B Surya Prasath
- Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, USA
| | - Yizhao Ni
- Cincinnati Children’s Hospital Medical Center, USA
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21
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Lv H, Shi L, Berkenpas JW, Dao FY, Zulfiqar H, Ding H, Zhang Y, Yang L, Cao R. Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design. Brief Bioinform 2021; 22:bbab320. [PMID: 34410360 PMCID: PMC8511807 DOI: 10.1093/bib/bbab320] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has led to a dramatic loss of human life worldwide. Despite many efforts, the development of effective drugs and vaccines for this novel virus will take considerable time. Artificial intelligence (AI) and machine learning (ML) offer promising solutions that could accelerate the discovery and optimization of new antivirals. Motivated by this, in this paper, we present an extensive survey on the application of AI and ML for combating COVID-19 based on the rapidly emerging literature. Particularly, we point out the challenges and future directions associated with state-of-the-art solutions to effectively control the COVID-19 pandemic. We hope that this review provides researchers with new insights into the ways AI and ML fight and have fought the COVID-19 outbreak.
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Affiliation(s)
- Hao Lv
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lei Shi
- Department of Spine Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200433, China
| | | | - Fu-Ying Dao
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hasan Zulfiqar
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Liming Yang
- Department of Pathophysiology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma 98447, USA
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22
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Brunk F, Moritz A, Nelde A, Bilich T, Casadei N, Fraschka SAK, Heitmann JS, Hörber S, Peter A, Rammensee H, Singh H, Walz J, Maurer D, Wagner C. SARS-CoV-2-reactive T-cell receptors isolated from convalescent COVID-19 patients confer potent T-cell effector function. Eur J Immunol 2021; 51:2651-2664. [PMID: 34424997 PMCID: PMC8646365 DOI: 10.1002/eji.202149290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/25/2021] [Indexed: 11/25/2022]
Abstract
Both B cells and T cells are involved in an effective immune response to SARS-CoV-2, the disease-causing virus of COVID-19. While B cells-with the indispensable help of CD4+ T cells-are essential to generate neutralizing antibodies, T cells on their own have been recognized as another major player in effective anti-SARS-CoV-2 immunity. In this report, we provide insights into the characteristics of individual HLA-A*02:01- and HLA-A*24:02-restricted SARS-CoV-2-reactive TCRs, isolated from convalescent COVID-19 patients. We observed that SARS-CoV-2-reactive T-cell populations were clearly detectable in convalescent samples and that TCRs isolated from these T cell clones were highly functional upon ectopic re-expression. The SARS-CoV-2-reactive TCRs described in this report mediated potent TCR signaling in reporter assays with low nanomolar EC50 values. We further demonstrate that these SARS-CoV-2-reactive TCRs conferred powerful T-cell effector function to primary CD8+ T cells as evident by a robust anti-SARS-CoV-2 IFN-γ response and in vitro cytotoxicity. We also provide an example of a long-lasting anti-SARS-CoV-2 memory response by reisolation of one of the retrieved TCRs 5 months after initial sampling. Taken together, these findings contribute to a better understanding of anti-SARS-CoV-2 T-cell immunity and may contribute to paving the way toward immunotherapeutics approaches targeting SARS-CoV-2.
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Affiliation(s)
| | | | - Annika Nelde
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Nicolas Casadei
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Sabine A. K. Fraschka
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Sebastian Hörber
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Andreas Peter
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Hans‐Georg Rammensee
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Partner Site TübingenTübingenGermany
| | | | - Juliane Walz
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- Dr. Margarete Fischer‐Bosch Institute of Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT)StuttgartGermany
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23
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Mohanty E, Mohanty A. Role of artificial intelligence in peptide vaccine design against RNA viruses. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100768. [PMID: 34722851 PMCID: PMC8536498 DOI: 10.1016/j.imu.2021.100768] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
RNA viruses have high rate of replication and mutation that help them adapt and change according to their environmental conditions. Many viral mutants are the cause of various severe and lethal diseases. Vaccines, on the other hand have the capacity to protect us from infectious diseases by eliciting antibody or cell-mediated immune responses that are pathogen-specific. While there are a few reviews pertaining to the use of artificial intelligence (AI) for SARS-COV-2 vaccine development, none focus on peptide vaccination for RNA viruses and the important role played by AI in it. Peptide vaccine which is slowly coming to be recognized as a safe and effective vaccination strategy has the capacity to overcome the mutant escape problem which is also being currently faced by SARS-COV-2 vaccines in circulation.Here we review the present scenario of peptide vaccines which are developed using mathematical and computational statistics methods to prevent the spread of disease caused by RNA viruses. We also focus on the importance and current stage of AI and mathematical evolutionary modeling using machine learning tools in the establishment of these new peptide vaccines for the control of viral disease.
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Affiliation(s)
- Eileena Mohanty
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar, Odisha, 751024, India
| | - Anima Mohanty
- School of Biotechnology (KSBT), KIIT University-2, Bhubaneswar, 751024, India
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24
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Deng H, Yan X, Yuan L. Human genetic basis of coronavirus disease 2019. Signal Transduct Target Ther 2021; 6:344. [PMID: 34545062 PMCID: PMC8450706 DOI: 10.1038/s41392-021-00736-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/28/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in considerable morbidity and mortality worldwide. COVID-19 incidence, severity, and mortality rates differ greatly between populations, genders, ABO blood groups, human leukocyte antigen (HLA) genotypes, ethnic groups, and geographic backgrounds. This highly heterogeneous SARS-CoV-2 infection is multifactorial. Host genetic factors such as variants in the angiotensin-converting enzyme gene (ACE), the angiotensin-converting enzyme 2 gene (ACE2), the transmembrane protease serine 2 gene (TMPRSS2), along with HLA genotype, and ABO blood group help to explain individual susceptibility, severity, and outcomes of COVID-19. This review is focused on COVID-19 clinical and viral characteristics, pathogenesis, and genetic findings, with particular attention on genetic diversity and variants. The human genetic basis could provide scientific bases for disease prediction and targeted therapy to address the COVID-19 scourge.
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Affiliation(s)
- Hao Deng
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China.
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China.
- Disease Genome Research Center, Central South University, Changsha, China.
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China.
| | - Xue Yan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
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25
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Uttamrao PP, Sathyaseelan C, Patro LPP, Rathinavelan T. Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach. Front Immunol 2021; 12:692937. [PMID: 34497604 PMCID: PMC8419283 DOI: 10.3389/fimmu.2021.692937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kills thousands of people worldwide every day, thus necessitating rapid development of countermeasures. Immunoinformatics analyses carried out here in search of immunodominant regions in recently identified SARS-CoV-2 unannotated open reading frames (uORFs) have identified eight linear B-cell, one conformational B-cell, 10 CD4+ T-cell, and 12 CD8+ T-cell promising epitopes. Among them, ORF9b B-cell and T-cell epitopes are the most promising followed by M.ext and ORF3c epitopes. ORF9b40-48 (CD8+ T-cell epitope) is found to be highly immunogenic and antigenic with the highest allele coverage. Furthermore, it has overlap with four potent CD4+ T-cell epitopes. Structure-based B-cell epitope prediction has identified ORF9b61-68 to be immunodominant, which partially overlaps with one of the linear B-cell epitopes (ORF9b65-69). ORF3c CD4+ T-cell epitopes (ORF3c2-16, ORF3c3-17, and ORF3c4-18) and linear B-cell epitope (ORF3c14-22) have also been identified as the candidate epitopes. Similarly, M.ext and 7a.iORF1 (overlap with M and ORF7a) proteins have promising immunogenic regions. By considering the level of antigen expression, four ORF9b and five M.ext epitopes are finally shortlisted as potent epitopes. Mutation analysis has further revealed that the shortlisted potent uORF epitopes are resistant to recurrent mutations. Additionally, four N-protein (expressed by canonical ORF) epitopes are found to be potent. Thus, SARS-CoV-2 uORF B-cell and T-cell epitopes identified here along with canonical ORF epitopes may aid in the design of a promising epitope-based polyvalent vaccine (when connected through appropriate linkers) against SARS-CoV-2. Such a vaccine can act as a bulwark against SARS-CoV-2, especially in the scenario of emergence of variants with recurring mutations in the spike protein.
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26
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Arora G, Joshi J, Mandal RS, Shrivastava N, Virmani R, Sethi T. Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19. Pathogens 2021; 10:1048. [PMID: 34451513 PMCID: PMC8399076 DOI: 10.3390/pathogens10081048] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.
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Affiliation(s)
- Gunjan Arora
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jayadev Joshi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
| | - Rahul Shubhra Mandal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Nitisha Shrivastava
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA;
| | - Richa Virmani
- Confo Therapeutics, Technologiepark 94, 9052 Ghent, Belgium;
| | - Tavpritesh Sethi
- Indraprastha Institute of Information Technology, New Delhi 110020, India;
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27
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Arora G, Joshi J, Mandal RS, Shrivastava N, Virmani R, Sethi T. Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19. Pathogens 2021; 10:1048. [PMID: 34451513 PMCID: PMC8399076 DOI: 10.3390/pathogens10081048,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.
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Affiliation(s)
- Gunjan Arora
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: or
| | - Jayadev Joshi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
| | - Rahul Shubhra Mandal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Nitisha Shrivastava
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA;
| | - Richa Virmani
- Confo Therapeutics, Technologiepark 94, 9052 Ghent, Belgium;
| | - Tavpritesh Sethi
- Indraprastha Institute of Information Technology, New Delhi 110020, India;
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Firouzi F, Farahani B, Daneshmand M, Grise K, Song J, Saracco R, Wang LL, Lo K, Angelov P, Soares E, Loh PS, Talebpour Z, Moradi R, Goodarzi M, Ashraf H, Talebpour M, Talebpour A, Romeo L, Das R, Heidari H, Pasquale D, Moody J, Woods C, Huang ES, Barnaghi P, Sarrafzadeh M, Li R, Beck KL, Isayev O, Sung N, Luo A. Harnessing the Power of Smart and Connected Health to Tackle COVID-19: IoT, AI, Robotics, and Blockchain for a Better World. IEEE INTERNET OF THINGS JOURNAL 2021; 8:12826-12846. [PMID: 35782886 PMCID: PMC8769005 DOI: 10.1109/jiot.2021.3073904] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/09/2021] [Accepted: 04/02/2021] [Indexed: 05/07/2023]
Abstract
As COVID-19 hounds the world, the common cause of finding a swift solution to manage the pandemic has brought together researchers, institutions, governments, and society at large. The Internet of Things (IoT), artificial intelligence (AI)-including machine learning (ML) and Big Data analytics-as well as Robotics and Blockchain, are the four decisive areas of technological innovation that have been ingenuity harnessed to fight this pandemic and future ones. While these highly interrelated smart and connected health technologies cannot resolve the pandemic overnight and may not be the only answer to the crisis, they can provide greater insight into the disease and support frontline efforts to prevent and control the pandemic. This article provides a blend of discussions on the contribution of these digital technologies, propose several complementary and multidisciplinary techniques to combat COVID-19, offer opportunities for more holistic studies, and accelerate knowledge acquisition and scientific discoveries in pandemic research. First, four areas, where IoT can contribute are discussed, namely: 1) tracking and tracing; 2) remote patient monitoring (RPM) by wearable IoT (WIoT); 3) personal digital twins (PDTs); and 4) real-life use case: ICT/IoT solution in South Korea. Second, the role and novel applications of AI are explained, namely: 1) diagnosis and prognosis; 2) risk prediction; 3) vaccine and drug development; 4) research data set; 5) early warnings and alerts; 6) social control and fake news detection; and 7) communication and chatbot. Third, the main uses of robotics and drone technology are analyzed, including: 1) crowd surveillance; 2) public announcements; 3) screening and diagnosis; and 4) essential supply delivery. Finally, we discuss how distributed ledger technologies (DLTs), of which blockchain is a common example, can be combined with other technologies for tackling COVID-19.
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Affiliation(s)
- Farshad Firouzi
- Electrical and Computer Engineering DepartmentDuke University Durham NC 27708 USA
| | - Bahar Farahani
- Cyberspace Research Institute, Shahid Beheshti University Tehran 1983969411 Iran
| | - Mahmoud Daneshmand
- Business Intelligence and AnalyticsStevens Institute of Technology Hoboken NJ 07030 USA
| | - Kathy Grise
- IEEE Future Directions Piscataway NJ 08854 USA
| | - Jaeseung Song
- Department of Computer and Information SecuritySejong University Seoul 15600 South Korea
| | | | - Lucy Lu Wang
- Allen Institute for Artificial Intelligence Seattle WA 98112 USA
| | - Kyle Lo
- Allen Institute for Artificial Intelligence Seattle WA 98112 USA
| | - Plamen Angelov
- School of Computing and CommunicationsLancaster University Lancashire LA1 4YW U.K
| | - Eduardo Soares
- School of Computing and CommunicationsLancaster University Lancashire LA1 4YW U.K
| | - Po-Shen Loh
- Department of Mathematical SciencesCarnegie Mellon University Pittsburgh PA 15213 USA
| | - Zeynab Talebpour
- Cyberspace Research Institute, Shahid Beheshti University Tehran 1983969411 Iran
| | - Reza Moradi
- Cyberspace Research Institute, Shahid Beheshti University Tehran 1983969411 Iran
| | - Mohsen Goodarzi
- Cyberspace Research Institute, Shahid Beheshti University Tehran 1983969411 Iran
| | | | | | - Alireza Talebpour
- Cyberspace Research Institute, Shahid Beheshti University Tehran 1983969411 Iran
| | - Luca Romeo
- Department of Information EngineeringUniversit Politecnica delle Marche 60121 Ancona Italy
| | - Rupam Das
- James Watt School of EngineeringUniversity of Glasgow Glasgow G12 8QQ U.K
| | - Hadi Heidari
- James Watt School of EngineeringUniversity of Glasgow Glasgow G12 8QQ U.K
| | - Dana Pasquale
- School of Medicine and Duke HealthDuke University Durham NC 27708 USA
| | - James Moody
- School of Medicine and Duke HealthDuke University Durham NC 27708 USA
| | - Chris Woods
- School of Medicine and Duke HealthDuke University Durham NC 27708 USA
| | - Erich S Huang
- School of Medicine and Duke HealthDuke University Durham NC 27708 USA
| | - Payam Barnaghi
- Department of Brain SciencesImperial College London London SW7 2AZ U.K
- U.K. Dementia Research Institute London U.K
| | - Majid Sarrafzadeh
- Computer Science Department & Electrical and Computer Engineering DepartmentUniversity of California at Los Angeles Los Angeles CA 90095 USA
| | - Ron Li
- Department of MedicineStanford University School of Medicine Stanford CA 94305 USA
| | | | - Olexandr Isayev
- Department of ChemistryCarnegie Mellon University Pittsburgh PA 15213 USA
| | - Nakmyoung Sung
- Korea Electronics Technology Institute Seongnam 13509 South Korea
| | - Alan Luo
- Computer Science DepartmentStanford University Stanford CA 94305 USA
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Schindler E, Dribus M, Duffy BF, Hock K, Farnsworth CW, Gragert L, Liu C. HLA genetic polymorphism in patients with Coronavirus Disease 2019 in Midwestern United States. HLA 2021; 98:370-379. [PMID: 34338446 PMCID: PMC8429120 DOI: 10.1111/tan.14387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022]
Abstract
The experience of individuals with Coronavirus Disease 2019 (COVID‐19) ranges from asymptomatic to life threatening multi‐organ dysfunction. Specific HLA alleles may affect the predisposition to severe COVID‐19 because of their role in presenting viral peptides to launch the adaptive immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). In this population‐based case–control study in the midwestern United States, we performed high‐resolution HLA typing of 234 cases hospitalized for COVID‐19 in the St. Louis metropolitan area and compared their HLA allele frequencies with those of 22,000 matched controls from the National Marrow Donor Program (NMDP). We identified two predisposing alleles, HLA‐DRB1*08:02 in the Hispanic group (OR = 9.0, 95% confidence interval: 2.2–37.9; adjusted p = 0.03) and HLA‐A*30:02 in younger African Americans with ages below the median (OR = 2.2, 1.4–3.6; adjusted p = 0.01), and several candidate alleles with potential associations with COVID‐19 in African American, White, and Hispanic groups. We also detected risk‐associated amino acid residues in the peptide binding grooves of some of these alleles, suggesting the presence of functional associations. These findings support the notion that specific HLA alleles may be protective or predisposing factors to COVID‐19. Future consortium analysis of pooled cases and controls is warranted to validate and extend these findings, and correlation with viral peptide binding studies will provide additional evidence for the functional association between HLA alleles and COVID‐19.
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Affiliation(s)
- Emily Schindler
- Department of Laboratory Medicine, Mercy Hospital, St. Louis, Missouri, USA
| | - Marian Dribus
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, USA
| | - Karl Hock
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher W Farnsworth
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Loren Gragert
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Prasad K, Kumar V. Artificial intelligence-driven drug repurposing and structural biology for SARS-CoV-2. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100042. [PMID: 34870150 PMCID: PMC8317454 DOI: 10.1016/j.crphar.2021.100042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
It has been said that COVID-19 is a generational challenge in many ways. But, at the same time, it becomes a catalyst for collective action, innovation, and discovery. Realizing the full potential of artificial intelligence (AI) for structure determination of unknown proteins and drug discovery are some of these innovations. Potential applications of AI include predicting the structure of the infectious proteins, identifying drugs that may be effective in targeting these proteins, and proposing new chemical compounds for further testing as potential drugs. AI and machine learning (ML) allow for rapid drug development including repurposing existing drugs. Algorithms were used to search for novel or approved antiviral drugs capable of inhibiting SARS-CoV-2. This paper presents a survey of AI and ML methods being used in various biochemistry of SARS-CoV-2, from structure to drug development, in the fight against the deadly COVID-19 pandemic. It is envisioned that this study will provide AI/ML researchers and the wider community an overview of the current status of AI applications particularly in structural biology, drug repurposing, and development, and motivate researchers in harnessing AI potentials in the fight against COVID-19.
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Affiliation(s)
- Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
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31
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Copley HC, Gragert L, Leach AR, Kosmoliaptsis V. Influence of HLA Class II Polymorphism on Predicted Cellular Immunity Against SARS-CoV-2 at the Population and Individual Level. Front Immunol 2021; 12:669357. [PMID: 34349756 PMCID: PMC8327207 DOI: 10.3389/fimmu.2021.669357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/28/2021] [Indexed: 01/16/2023] Open
Abstract
Development of adaptive immunity after COVID-19 and after vaccination against SARS-CoV-2 is predicated on recognition of viral peptides, presented on HLA class II molecules, by CD4+ T-cells. We capitalised on extensive high-resolution HLA data on twenty five human race/ethnic populations to investigate the role of HLA polymorphism on SARS-CoV-2 immunogenicity at the population and individual level. Within populations, we identify wide inter-individual variability in predicted peptide presentation from structural, non-structural and accessory SARS-CoV-2 proteins, according to individual HLA genotype. However, we find similar potential for anti-SARS-CoV-2 cellular immunity at the population level suggesting that HLA polymorphism is unlikely to account for observed disparities in clinical outcomes after COVID-19 among different race/ethnic groups. Our findings provide important insight on the potential role of HLA polymorphism on development of protective immunity after SARS-CoV-2 infection and after vaccination and a firm basis for further experimental studies in this field.
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Affiliation(s)
- Hannah C. Copley
- Department of Surgery, Addenbrooke’s Hospital, University of Cambridge, Cambridge, United Kingdom
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Loren Gragert
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA, United States
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, United States
| | - Andrew R. Leach
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Vasilis Kosmoliaptsis
- Department of Surgery, Addenbrooke’s Hospital, University of Cambridge, Cambridge, United Kingdom
- National Institute of Health Research (NIHR) Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
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32
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Grifoni A, Sidney J, Vita R, Peters B, Crotty S, Weiskopf D, Sette A. SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19. Cell Host Microbe 2021; 29:1076-1092. [PMID: 34237248 PMCID: PMC8139264 DOI: 10.1016/j.chom.2021.05.010] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Over the past year, numerous studies in the peer reviewed and preprint literature have reported on the virological, epidemiological and clinical characteristics of the coronavirus, SARS-CoV-2. To date, 25 studies have investigated and identified SARS-CoV-2-derived T cell epitopes in humans. Here, we review these recent studies, how they were performed, and their findings. We review how epitopes identified throughout the SARS-CoV2 proteome reveal significant correlation between number of epitopes defined and size of the antigen provenance. We also report additional analysis of SARS-CoV-2 human CD4 and CD8 T cell epitope data compiled from these studies, identifying 1,400 different reported SARS-CoV-2 epitopes and revealing discrete immunodominant regions of the virus and epitopes that are more prevalently recognized. This remarkable breadth of epitope repertoire has implications for vaccine design, cross-reactivity, and immune escape by SARS-CoV-2 variants.
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Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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Nguyen DC, Ding M, Pathirana PN, Seneviratne A. Blockchain and AI-Based Solutions to Combat Coronavirus (COVID-19)-Like Epidemics: A Survey. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:95730-95753. [PMID: 34812398 PMCID: PMC8545197 DOI: 10.1109/access.2021.3093633] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/27/2021] [Indexed: 05/02/2023]
Abstract
The beginning of 2020 has seen the emergence of coronavirus outbreak caused by a novel virus called SARS-CoV-2. The sudden explosion and uncontrolled worldwide spread of COVID-19 show the limitations of existing healthcare systems in timely handling public health emergencies. In such contexts, innovative technologies such as blockchain and Artificial Intelligence (AI) have emerged as promising solutions for fighting coronavirus epidemic. In particular, blockchain can combat pandemics by enabling early detection of outbreaks, ensuring the ordering of medical data, and ensuring reliable medical supply chain during the outbreak tracing. Moreover, AI provides intelligent solutions for identifying symptoms caused by coronavirus for treatments and supporting drug manufacturing. Therefore, we present an extensive survey on the use of blockchain and AI for combating COVID-19 epidemics. First, we introduce a new conceptual architecture which integrates blockchain and AI for fighting COVID-19. Then, we survey the latest research efforts on the use of blockchain and AI for fighting COVID-19 in various applications. The newly emerging projects and use cases enabled by these technologies to deal with coronavirus pandemic are also presented. A case study is also provided using federated AI for COVID-19 detection. Finally, we point out challenges and future directions that motivate more research efforts to deal with future coronavirus-like epidemics.
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Affiliation(s)
- Dinh C. Nguyen
- School of EngineeringDeakin UniversityWaurn PondsVIC3216Australia
| | | | | | - Aruna Seneviratne
- School of Electrical Engineering and TelecommunicationsUniversity of New South Wales (UNSW)SydneyNSW2052Australia
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Ma Y, Liu F, Lin T, Chen L, Jiang A, Tian G, Nielsen M, Wang M. Large-scale identification of T cell epitopes derived from SARS-CoV-2 for the development of peptide vaccines against COVID-19. J Infect Dis 2021; 224:956-966. [PMID: 34145459 DOI: 10.1093/infdis/jiab324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/16/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Coronavirus disease-19 (COVID-19) continues to be a major public health challenge globally. The identification of SARS-CoV-2-derived T cell epitopes is of critical importance for peptide vaccines or diagnostic tools of COVID-19. METHODS In this study, a number of SARS-CoV-2-derived HLA-I binding peptides were predicted by NetMHCpan-4.1 and selected by Popcover to achieve pancoverage of the Chinese population. The top 5 ranked peptides derived from each protein of SARS-CoV-2 were then evaluated using PBMCs from unexposed individuals (negative for SARS-CoV-2 IgG). RESULTS Seven epitopes derived from 4 SARS-CoV-2 proteins were identified. Interestingly, most (5 out of 7) of the SARS-CoV-2-derived peptides with predicted affinities for HLA-I molecules were identified as HLA-II-restricted epitopes and induced CD4+ T cell-dependent responses. These results complete missing pieces of pre-existing SARS-CoV-2-specific T cells and suggest that pre-existing T cells targeting all SARS-CoV-2-encoded proteins can be discovered in unexposed populations. CONCLUSIONS In summary, in the current study, we present an alternative and effective strategy for the identification of T cell epitopes of SARS-CoV-2 in healthy subjects, which may indicate an important role in the development of peptide vaccines for COVID-19.
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Affiliation(s)
- Yipeng Ma
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Fenglan Liu
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Tong Lin
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Lei Chen
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Aixin Jiang
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Geng Tian
- Department of Oncology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Mingjun Wang
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
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35
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Quadeer AA, Ahmed SF, McKay MR. Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform. Cell Rep Med 2021; 2:100312. [PMID: 34056627 PMCID: PMC8139281 DOI: 10.1016/j.xcrm.2021.100312] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 01/18/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Knowledge of the epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) targeted by T cells in recovered (convalescent) individuals is important for understanding T cell immunity against coronavirus disease 2019 (COVID-19). This information can aid development and assessment of COVID-19 vaccines and inform novel diagnostic technologies. Here, we provide a unified description and meta-analysis of SARS-CoV-2 T cell epitopes compiled from 18 studies of cohorts of individuals recovered from COVID-19 (852 individuals in total). Our analysis demonstrates the broad diversity of T cell epitopes that have been recorded for SARS-CoV-2. A large majority are seemingly unaffected by current variants of concern. We identify a set of 20 immunoprevalent epitopes that induced T cell responses in multiple cohorts and in a large fraction of tested individuals. The landscape of SARS-CoV-2 T cell epitopes we describe can help guide immunological studies, including those related to vaccines and diagnostics. A web-based platform has been developed to help complement these efforts.
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Affiliation(s)
- Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Syed Faraz Ahmed
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Matthew R. McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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36
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Piel LMW, Durfee CJ, White SN. Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species. BMC Bioinformatics 2021; 22:296. [PMID: 34078271 PMCID: PMC8170629 DOI: 10.1186/s12859-021-04181-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/10/2021] [Indexed: 12/29/2022] Open
Abstract
Background Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surface isolated proteins confer protection but can produce a reactogenic immune responses. Thereby a protective vaccine that does not cause aberrant immune reactions is required. The critical role of T-cell immunity in control of C. burnetii has been made clear, since either CD8+ or CD4+ T cells can empower clearance. The purpose of this study was to identify C. burnetii proteins bearing epitopes that interact with major histocompatibility complexes (MHC) from multiple host species (human, mouse, and cattle). Results Of the annotated 1815 proteins from the Nine Mile Phase I (RSA 493) assembly, 402 proteins were removed from analysis due to a lack of inter-isolate conservation. An additional 391 proteins were eliminated from assessment to avoid potential autoimmune responses due to the presence of host homology. We analyzed the remaining 1022 proteins for their ability to produce peptides that bind MHCI or MHCII. MHCI and MHCII predicted epitopes were filtered and compared between species yielding 777 MHCI epitopes and 453 MHCII epitopes. These epitopes were further examined for presentation by both MHCI and MHCII, and for proteins that contained multiple epitopes. There were 31 epitopes that overlapped positionally between MHCI and MHCII across host species. Of these, there were 9 epitopes represented within proteins containing ≥ 5 total epitopes, where an additional 24 proteins were also epitope dense. In all, 55 proteins were found to contain high scoring T-cell epitopes. Besides the well-studied protein Com1, most identified proteins were novel when compared to previously studied vaccine candidates. Conclusion These data represent the first proteome-wide evaluation of C. burnetii peptide epitopes. Furthermore, the inclusion of human, mouse, and bovine data capture a range of hosts for this zoonotic pathogen plus an important model organism. This work provides new vaccine targets for future vaccination efforts and enhances opportunities for selecting multiple T-cell epitope types to include within a vaccine. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04181-w.
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Affiliation(s)
| | - Codie J Durfee
- USDA-ARS Animal Disease Research Unit, Pullman, WA, 99164, USA
| | - Stephen N White
- USDA-ARS Animal Disease Research Unit, Pullman, WA, 99164, USA. .,Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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Juanes-Velasco P, Landeira-Viñuela A, Acebes-Fernandez V, Hernández ÁP, Garcia-Vaquero ML, Arias-Hidalgo C, Bareke H, Montalvillo E, Gongora R, Fuentes M. Deciphering Human Leukocyte Antigen Susceptibility Maps From Immunopeptidomics Characterization in Oncology and Infections. Front Cell Infect Microbiol 2021; 11:642583. [PMID: 34123866 PMCID: PMC8195621 DOI: 10.3389/fcimb.2021.642583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [HLA] A, B, and C) may affect susceptibility to many diseases such as cancer, auto-immune or infectious diseases. Individual genetic variation may help to explain different immune responses to microorganisms across a population. HLA typing can be fast and inexpensive; however, deciphering peptides loaded on MHC-I and II which are presented to T cells, require the design and development of high-sensitivity methodological approaches and subsequently databases. Hence, these novel strategies and databases could help in the generation of vaccines using these potential immunogenic peptides and in identifying high-risk HLA types to be prioritized for vaccination programs. Herein, the recent developments and approaches, in this field, focusing on the identification of immunogenic peptides have been reviewed and the next steps to promote their translation into biomedical and clinical practice are discussed.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Vanessa Acebes-Fernandez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina L. Garcia-Vaquero
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Halin Bareke
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Enrique Montalvillo
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafael Gongora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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Gangaev A, Ketelaars SLC, Isaeva OI, Patiwael S, Dopler A, Hoefakker K, De Biasi S, Gibellini L, Mussini C, Guaraldi G, Girardis M, Ormeno CMPT, Hekking PJM, Lardy NM, Toebes M, Balderas R, Schumacher TN, Ovaa H, Cossarizza A, Kvistborg P. Identification and characterization of a SARS-CoV-2 specific CD8 + T cell response with immunodominant features. Nat Commun 2021; 12:2593. [PMID: 33972535 PMCID: PMC8110804 DOI: 10.1038/s41467-021-22811-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a continuous challenge worldwide, and there is an urgent need to map the landscape of immunogenic and immunodominant epitopes recognized by CD8+ T cells. Here, we analyze samples from 31 patients with COVID-19 for CD8+ T cell recognition of 500 peptide-HLA class I complexes, restricted by 10 common HLA alleles. We identify 18 CD8+ T cell recognized SARS-CoV-2 epitopes, including an epitope with immunodominant features derived from ORF1ab and restricted by HLA-A*01:01. In-depth characterization of SARS-CoV-2-specific CD8+ T cell responses of patients with acute critical and severe disease reveals high expression of NKG2A, lack of cytokine production and a gene expression profile inhibiting T cell re-activation and migration while sustaining survival. SARS-CoV-2-specific CD8+ T cell responses are detectable up to 5 months after recovery from critical and severe disease, and these responses convert from dysfunctional effector to functional memory CD8+ T cells during convalescence.
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Affiliation(s)
- Anastasia Gangaev
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Steven L. C. Ketelaars
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Olga I. Isaeva
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Sanne Patiwael
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Anna Dopler
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Kelly Hoefakker
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Sara De Biasi
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Lara Gibellini
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Cristina Mussini
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Giovanni Guaraldi
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Massimo Girardis
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Cami M. P. Talavera Ormeno
- grid.10419.3d0000000089452978Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, South Holland The Netherlands
| | - Paul J. M. Hekking
- grid.10419.3d0000000089452978Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, South Holland The Netherlands
| | - Neubury M. Lardy
- grid.417732.40000 0001 2234 6887Department of Immunogenetics, Sanquin Diagnostics B.V., Amsterdam, North Holland The Netherlands
| | - Mireille Toebes
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Robert Balderas
- grid.420052.10000 0004 0543 6807Department of Biological Sciences, BD Biosciences, San Jose, CA USA
| | - Ton N. Schumacher
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
| | - Huib Ovaa
- grid.10419.3d0000000089452978Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, South Holland The Netherlands
| | - Andrea Cossarizza
- grid.7548.e0000000121697570University of Modena and Reggio Emilia School of Medicine, Modena, Emilia Romagna Italy
| | - Pia Kvistborg
- grid.430814.aDivision of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, North Holland The Netherlands
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39
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Hwang W, Lei W, Katritsis NM, MacMahon M, Chapman K, Han N. Current and prospective computational approaches and challenges for developing COVID-19 vaccines. Adv Drug Deliv Rev 2021; 172:249-274. [PMID: 33561453 PMCID: PMC7871111 DOI: 10.1016/j.addr.2021.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019 and is a coronavirus which is zoonotic in origin. As it spread around the world there has been an unprecedented effort in developing effective vaccines. Computational methods can be used to speed up the long and costly process of vaccine development. Antigen selection, epitope prediction, and toxicity and allergenicity prediction are areas in which computational tools have already been applied as part of reverse vaccinology for SARS-CoV-2 vaccine development. However, there is potential for computational methods to assist further. We review approaches which have been used and highlight additional bioinformatic approaches and PK modelling as in silico methods which may be useful for SARS-CoV-2 vaccine design but remain currently unexplored. As more novel viruses with pandemic potential are expected to arise in future, these techniques are not limited to application to SARS-CoV-2 but also useful to rapidly respond to novel emerging viruses.
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Affiliation(s)
- Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Winnie Lei
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Nicholas M Katritsis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Méabh MacMahon
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK; Centre for Therapeutics Discovery, LifeArc, Stevenage, UK
| | - Kathryn Chapman
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
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40
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Piccialli F, di Cola VS, Giampaolo F, Cuomo S. The Role of Artificial Intelligence in Fighting the COVID-19 Pandemic. INFORMATION SYSTEMS FRONTIERS : A JOURNAL OF RESEARCH AND INNOVATION 2021; 23:1467-1497. [PMID: 33935585 PMCID: PMC8072097 DOI: 10.1007/s10796-021-10131-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/28/2021] [Indexed: 05/25/2023]
Abstract
The first few months of 2020 have profoundly changed the way we live our lives and carry out our daily activities. Although the widespread use of futuristic robotaxis and self-driving commercial vehicles has not yet become a reality, the COVID-19 pandemic has dramatically accelerated the adoption of Artificial Intelligence (AI) in different fields. We have witnessed the equivalent of two years of digital transformation compressed into just a few months. Whether it is in tracing epidemiological peaks or in transacting contactless payments, the impact of these developments has been almost immediate, and a window has opened up on what is to come. Here we analyze and discuss how AI can support us in facing the ongoing pandemic. Despite the numerous and undeniable contributions of AI, clinical trials and human skills are still required. Even if different strategies have been developed in different states worldwide, the fight against the pandemic seems to have found everywhere a valuable ally in AI, a global and open-source tool capable of providing assistance in this health emergency. A careful AI application would enable us to operate within this complex scenario involving healthcare, society and research.
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Affiliation(s)
- Francesco Piccialli
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
| | - Vincenzo Schiano di Cola
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, 80125 Italy
| | - Fabio Giampaolo
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
| | - Salvatore Cuomo
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
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41
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Gao A, Chen Z, Amitai A, Doelger J, Mallajosyula V, Sundquist E, Pereyra Segal F, Carrington M, Davis MM, Streeck H, Chakraborty AK, Julg B. Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2. iScience 2021; 24:102311. [PMID: 33748696 PMCID: PMC7956900 DOI: 10.1016/j.isci.2021.102311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe a physics-based learning model for predicting the immunogenicity of cytotoxic T lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in human immunodeficiency virus infection. Its accuracy was tested against experimental data from patients with COVID-19. Our model predicts that only some SARS-CoV-2 epitopes predicted to bind to HLA molecules are immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but those from the SARS-CoV-2 spike protein alone are unlikely to do so. Our model also predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to seasonal coronaviruses circulating in the population and such cross-reactive CD8+ T cells can indeed be detected in prepandemic blood donors, suggesting that some level of CTL immunity against COVID-19 may be present in some individuals before SARS-CoV-2 infection.
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Affiliation(s)
- Ang Gao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhilin Chen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | - Assaf Amitai
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Julia Doelger
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily Sundquist
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hendrik Streeck
- Institut für Virologie, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Arup K. Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
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42
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Sohail MS, Ahmed SF, Quadeer AA, McKay MR. In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives. Adv Drug Deliv Rev 2021; 171:29-47. [PMID: 33465451 PMCID: PMC7832442 DOI: 10.1016/j.addr.2021.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/31/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Growing evidence suggests that T cells may play a critical role in combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, COVID-19 vaccines that can elicit a robust T cell response may be particularly important. The design, development and experimental evaluation of such vaccines is aided by an understanding of the landscape of T cell epitopes of SARS-CoV-2, which is largely unknown. Due to the challenges of identifying epitopes experimentally, many studies have proposed the use of in silico methods. Here, we present a review of the in silico methods that have been used for the prediction of SARS-CoV-2 T cell epitopes. These methods employ a diverse set of technical approaches, often rooted in machine learning. A performance comparison is provided based on the ability to identify a specific set of immunogenic epitopes that have been determined experimentally to be targeted by T cells in convalescent COVID-19 patients, shedding light on the relative performance merits of the different approaches adopted by the in silico studies. The review also puts forward perspectives for future research directions.
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Affiliation(s)
- Muhammad Saqib Sohail
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Syed Faraz Ahmed
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
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43
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Dijkstra JM, Frenette AP, Dixon B. Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses. F1000Res 2021; 10:196. [PMID: 34026045 PMCID: PMC8108557 DOI: 10.12688/f1000research.51479.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In the spring of 2020, we and others hypothesized that T cells in COVID-19 patients may recognize identical protein fragments shared between the coronaviruses of the common cold and COVID-19 and thereby confer cross-virus immune memory. Here, we look at this issue by screening studies that, since that time, have experimentally addressed COVID-19 associated T cell specificities. Currently, the identical T cell epitope shared between COVID-19 and common cold coronaviruses most convincingly identified as immunogenic is the CD8 + T cell epitope VYIGDPAQL if presented by the MHC class I allele HLA-A*24:02. The HLA-A*24:02 allele is found in the majority of Japanese individuals and several indigenous populations in Asia, Oceania, and the Americas. In combination with histories of common cold infections, HLA-A*24:02 may affect their protection from COVID-19.
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Affiliation(s)
- Johannes M. Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health Universit, Toyoake-shi, 470-1192, Japan
| | - Aaron P. Frenette
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
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44
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Kared H, Redd AD, Bloch EM, Bonny TS, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell EW, Bettinotti MP, Benner SE, Patel EU, Littlefield K, Laeyendecker O, Shoham S, Sullivan D, Casadevall A, Pekosz A, Nardin A, Fehlings M, Tobian AA, Quinn TC. SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals. J Clin Invest 2021; 131:145476. [PMID: 33427749 DOI: 10.1172/jci145476] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Characterization of the T cell response in individuals who recover from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 coronavirus disease 2019 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis and from humoral and inflammatory responses. There were 132 SARS-CoV-2-specific CD8+ T cell responses detected across 6 different HLAs, corresponding to 52 unique epitope reactivities. CD8+ T cell responses were detected in almost all convalescent individuals and were directed against several structural and nonstructural target epitopes from the entire SARS-CoV-2 proteome. A unique phenotype for SARS-CoV-2-specific T cells was observed that was distinct from other common virus-specific T cells detected in the same cross-sectional sample and characterized by early differentiation kinetics. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem cell and transitional memory states (subsets), which may be key to developing durable protection.
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Affiliation(s)
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tania S Bonny
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - Evan W Newell
- ImmunoScape, Singapore, Singapore.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Maria P Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eshan U Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Epidemiology and
| | - Kirsten Littlefield
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | | | - David Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Aaron Ar Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
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45
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Nguyen DC, Ding M, Pathirana PN, Seneviratne A. Blockchain and AI-Based Solutions to Combat Coronavirus (COVID-19)-Like Epidemics: A Survey. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:95730-95753. [PMID: 34812398 DOI: 10.20944/preprints202004.0325.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
The beginning of 2020 has seen the emergence of coronavirus outbreak caused by a novel virus called SARS-CoV-2. The sudden explosion and uncontrolled worldwide spread of COVID-19 show the limitations of existing healthcare systems in timely handling public health emergencies. In such contexts, innovative technologies such as blockchain and Artificial Intelligence (AI) have emerged as promising solutions for fighting coronavirus epidemic. In particular, blockchain can combat pandemics by enabling early detection of outbreaks, ensuring the ordering of medical data, and ensuring reliable medical supply chain during the outbreak tracing. Moreover, AI provides intelligent solutions for identifying symptoms caused by coronavirus for treatments and supporting drug manufacturing. Therefore, we present an extensive survey on the use of blockchain and AI for combating COVID-19 epidemics. First, we introduce a new conceptual architecture which integrates blockchain and AI for fighting COVID-19. Then, we survey the latest research efforts on the use of blockchain and AI for fighting COVID-19 in various applications. The newly emerging projects and use cases enabled by these technologies to deal with coronavirus pandemic are also presented. A case study is also provided using federated AI for COVID-19 detection. Finally, we point out challenges and future directions that motivate more research efforts to deal with future coronavirus-like epidemics.
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Affiliation(s)
- Dinh C Nguyen
- School of EngineeringDeakin University Waurn Ponds VIC 3216 Australia
| | - Ming Ding
- Data61CSIRO Eveleigh NSW 2015 Australia
| | | | - Aruna Seneviratne
- School of Electrical Engineering and TelecommunicationsUniversity of New South Wales (UNSW) Sydney NSW 2052 Australia
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46
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Poongodi M, Malviya M, Hamdi M, Rauf HT, Kadry S, Thinnukool O. The Recent Technologies to Curb the Second-Wave of COVID-19 Pandemic. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:97906-97928. [PMID: 34812400 PMCID: PMC8545196 DOI: 10.1109/access.2021.3094400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 05/06/2023]
Abstract
Different epidemics, specially Coronavirus, have caused critical misfortunes in various fields like monetary deprivation, survival conditions, thus diminishing the overall individual fulfillment. Various worldwide associations and different hierarchies of government fraternity are endeavoring to offer the necessary assistance in eliminating the infection impacts but unfortunately standing up to the non-appearance of resources and expertise. In contrast to all other pandemics, Coronavirus has proven to exhibit numerous requirements such that curated appropriation and determination of innovations are required to deal with the vigorous undertakings, which include precaution, detection, and medication. Innovative advancements are essential for the subsequent pandemics where-in the forthcoming difficulties can indeed be approached to such a degree that it facilitates constructive solutions more comprehensively. In this study, futuristic and emerging innovations are analyzed, improving COVID-19 effects for the general public. Large data sets need to be advanced so that extensive models related to deep analysis can be used to combat Coronavirus infection, which can be done by applying Artificial intelligence techniques such as Natural Language Processing (NLP), Machine Learning (ML), and Computer vision to varying processing files. This article aims to furnish variation sets of innovations that can be utilized to eliminate COVID-19 and serve as a resource for the coming generations. At last, elaboration associated with future state-of-the-art technologies and the attainable sectors of AI methodologies has been mentioned concerning the post-COVID-19 world to enable the different ideas for dealing with the pandemic-based difficulties.
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Affiliation(s)
- M Poongodi
- College of Science and EngineeringHamad Bin Khalifa University, Qatar Foundation Doha Qatar
| | - Mohit Malviya
- Department of CTO 5GWipro Ltd. Bengaluru 560035 India
| | - Mounir Hamdi
- College of Science and EngineeringHamad Bin Khalifa University, Qatar Foundation Doha Qatar
| | - Hafiz Tayyab Rauf
- Centre for Smart SystemsAI and Cybersecurity, Staffordshire University Stoke-on-Trent ST4 2DE U.K
| | - Seifedine Kadry
- Faculty of Applied Computing and TechnologyNoroff University College 4608 Kristiansand Norway
| | - Orawit Thinnukool
- Research Group of Embedded Systems and Mobile Application in Health Science, College of Arts, Media and TechnologyChiang Mai University Chiang Mai 50200 Thailand
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47
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Di Natale C, La Manna S, De Benedictis I, Brandi P, Marasco D. Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic. Front Pharmacol 2020; 11:578382. [PMID: 33343349 PMCID: PMC7744882 DOI: 10.3389/fphar.2020.578382] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
At the end of December 2019, an epidemic form of respiratory tract infection now named COVID-19 emerged in Wuhan, China. It is caused by a newly identified viral pathogen, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which can cause severe pneumonia and acute respiratory distress syndrome. On January 30, 2020, due to the rapid spread of infection, COVID-19 was declared as a global health emergency by the World Health Organization. Coronaviruses are enveloped RNA viruses belonging to the family of Coronaviridae, which are able to infect birds, humans and other mammals. The majority of human coronavirus infections are mild although already in 2003 and in 2012, the epidemics of SARS-CoV and Middle East Respiratory Syndrome coronavirus (MERS-CoV), respectively, were characterized by a high mortality rate. In this regard, many efforts have been made to develop therapeutic strategies against human CoV infections but, unfortunately, drug candidates have shown efficacy only into in vitro studies, limiting their use against COVID-19 infection. Actually, no treatment has been approved in humans against SARS-CoV-2, and therefore there is an urgent need of a suitable vaccine to tackle this health issue. However, the puzzled scenario of biological features of the virus and its interaction with human immune response, represent a challenge for vaccine development. As expected, in hundreds of research laboratories there is a running out of breath to explore different strategies to obtain a safe and quickly spreadable vaccine; and among others, the peptide-based approach represents a turning point as peptides have demonstrated unique features of selectivity and specificity toward specific targets. Peptide-based vaccines imply the identification of different epitopes both on human cells and virus capsid and the design of peptide/peptidomimetics able to counteract the primary host-pathogen interaction, in order to induce a specific host immune response. SARS-CoV-2 immunogenic regions are mainly distributed, as well as for other coronaviruses, across structural areas such as spike, envelope, membrane or nucleocapsid proteins. Herein, we aim to highlight the molecular basis of the infection and recent peptide-based vaccines strategies to fight the COVID-19 pandemic including their delivery systems.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano Di Tecnologia, Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB) and Dipartimento di Ingegneria Chimica, Dei Materiali e Della Produzione Industriale, University of Naples Federico II, Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | - Paola Brandi
- Centro Nacional De Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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