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Hamelin D, Scicluna M, Saadie I, Mostefai F, Grenier J, Baron C, Caron E, Hussin J. Predicting pathogen evolution and immune evasion in the age of artificial intelligence. Comput Struct Biotechnol J 2025; 27:1370-1382. [PMID: 40235636 PMCID: PMC11999473 DOI: 10.1016/j.csbj.2025.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 03/21/2025] [Accepted: 03/26/2025] [Indexed: 04/17/2025] Open
Abstract
The genomic diversification of viral pathogens during viral epidemics and pandemics represents a major adaptive route for infectious agents to circumvent therapeutic and public health initiatives. Historically, strategies to address viral evolution have relied on responding to emerging variants after their detection, leading to delays in effective public health responses. Because of this, a long-standing yet challenging objective has been to forecast viral evolution by predicting potentially harmful viral mutations prior to their emergence. The promises of artificial intelligence (AI) coupled with the exponential growth of viral data collection infrastructures spurred by the COVID-19 pandemic, have resulted in a research ecosystem highly conducive to this objective. Due to the COVID-19 pandemic accelerating the development of pandemic mitigation and preparedness strategies, many of the methods discussed here were designed in the context of SARS-CoV-2 evolution. However, most of these pipelines were intentionally designed to be adaptable across RNA viruses, with several strategies already applied to multiple viral species. In this review, we explore recent breakthroughs that have facilitated the forecasting of viral evolution in the context of an ongoing pandemic, with particular emphasis on deep learning architectures, including the promising potential of language models (LM). The approaches discussed here employ strategies that leverage genomic, epidemiologic, immunologic and biological information.
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Affiliation(s)
- D.J. Hamelin
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Mila - Quebec AI Institute, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - M. Scicluna
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Mila - Quebec AI Institute, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - I. Saadie
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - F. Mostefai
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Mila - Quebec AI Institute, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - J.C. Grenier
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
| | - C. Baron
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Mila - Quebec AI Institute, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - E. Caron
- CHU Sainte-Justine Research Center, Université de Montréal, Montréal, Quebec, Canada
- Yale Center for Immuno-Oncology, Yale Center for Systems and Engineering Immunology, Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - J.G. Hussin
- Montreal Heart Institute, Université de Montréal, Montréal, Quebec, Canada
- Mila - Quebec AI Institute, Montréal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
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2
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Zornikova K, Dianov D, Ivanova N, Davydova V, Nenasheva T, Fefelova E, Bogolyubova A. Features of Highly Homologous T-Cell Receptor Repertoire in the Immune Response to Mutations in Immunogenic Epitopes. Int J Mol Sci 2024; 25:12591. [PMID: 39684303 DOI: 10.3390/ijms252312591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 11/21/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
CD8+ T-cell immunity, mediated through interactions between human leukocyte antigen (HLA) and the T-cell receptor (TCR), plays a pivotal role in conferring immune memory and protection against viral infections. The emergence of SARS-CoV-2 variants presents a significant challenge to the existing population immunity. While numerous SARS-CoV-2 mutations have been associated with immune evasion from CD8+ T cells, the molecular effects of most mutations on epitope-specific TCR recognition remain largely unexplored, particularly for epitope-specific repertoires characterized by common TCRs. In this study, we investigated an HLA-A*24-restricted NYN epitope (Spike448-456) that elicits broad and highly homologous CD8+ T cell responses in COVID-19 patients. Eleven naturally occurring mutations in the NYN epitope, all of which retained cell surface presentation by HLA, were tested against four transgenic Jurkat reporter cell lines. Our findings demonstrate that, with the exception of L452R and the combined mutation L452Q + Y453F, these mutations have minimal impact on the avidity of recognition by NYN peptide-specific TCRs. Additionally, we observed that a similar TCR responded differently to mutant epitopes and demonstrated cross-reactivity to the unrelated VYF epitope (ORF3a112-120). The results contradict the idea that immune responses with limited receptor diversity are insufficient to provide protection against emerging variants.
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Affiliation(s)
- Ksenia Zornikova
- National Medical Research Center for Hematology, Moscow 125167, Russia
| | - Dmitry Dianov
- National Medical Research Center for Hematology, Moscow 125167, Russia
| | - Natalia Ivanova
- National Medical Research Center for Hematology, Moscow 125167, Russia
| | - Vassa Davydova
- National Medical Research Center for Hematology, Moscow 125167, Russia
| | - Tatiana Nenasheva
- National Medical Research Center for Hematology, Moscow 125167, Russia
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3
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Macchia I, La Sorsa V, Ciervo A, Ruspantini I, Negri D, Borghi M, De Angelis ML, Luciani F, Martina A, Taglieri S, Durastanti V, Altavista MC, Urbani F, Mancini F. T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects. Biomolecules 2024; 14:1217. [PMID: 39456150 PMCID: PMC11505848 DOI: 10.3390/biom14101217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 10/28/2024] Open
Abstract
COVID-19 remains a significant threat, particularly to vulnerable populations. The emergence of new variants necessitates the development of treatments and vaccines that induce both humoral and cellular immunity. This study aimed to identify potentially immunogenic SARS-CoV-2 peptides and to explore the intricate host-pathogen interactions involving peripheral immune responses, memory profiles, and various demographic, clinical, and lifestyle factors. Using in silico and experimental methods, we identified several CD8-restricted SARS-CoV-2 peptides that are either poorly studied or have previously unreported immunogenicity: fifteen from the Spike and three each from non-structural proteins Nsp1-2-3-16. A Spike peptide, LA-9, demonstrated a 57% response rate in ELISpot assays using PBMCs from 14 HLA-A*02:01 positive, vaccinated, and mild-COVID-19 recovered subjects, indicating its potential for diagnostics, research, and multi-epitope vaccine platforms. We also found that younger individuals, with fewer vaccine doses and longer intervals since infection, showed lower anti-Spike (ELISA) and anti-Wuhan neutralizing antibodies (pseudovirus assay), higher naïve T cells, and lower central memory, effector memory, and CD4hiCD8low T cells (flow cytometry) compared to older subjects. In our cohort, a higher prevalence of Vδ2-γδ and DN T cells, and fewer naïve CD8 T cells, seemed to correlate with strong cellular and lower anti-NP antibody responses and to associate with Omicron infection, absence of confusional state, and habitual sporting activity.
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Affiliation(s)
- Iole Macchia
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.M.); (M.L.D.A.); (S.T.)
| | - Valentina La Sorsa
- Research Promotion and Coordination Service, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Alessandra Ciervo
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.C.); (D.N.); (M.B.); (F.M.)
| | - Irene Ruspantini
- Core Facilities, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.C.); (D.N.); (M.B.); (F.M.)
| | - Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.C.); (D.N.); (M.B.); (F.M.)
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.M.); (M.L.D.A.); (S.T.)
| | - Francesca Luciani
- National Center for the Control and Evaluation of Medicines, Istituto Superiore di Sanità, 00161 Rome, Italy; (F.L.); (A.M.)
| | - Antonio Martina
- National Center for the Control and Evaluation of Medicines, Istituto Superiore di Sanità, 00161 Rome, Italy; (F.L.); (A.M.)
| | - Silvia Taglieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.M.); (M.L.D.A.); (S.T.)
| | - Valentina Durastanti
- Neurology Unit, San Filippo Neri Hospital, ASL RM1, 00135 Rome, Italy; (V.D.); (M.C.A.)
| | | | - Francesca Urbani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.M.); (M.L.D.A.); (S.T.)
| | - Fabiola Mancini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.C.); (D.N.); (M.B.); (F.M.)
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4
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Jansen JM, Meineke R, Molle A, van de Sandt CE, Saletti G, Rimmelzwaan GF. Selective pressure mediated by influenza virus M1 58-66 epitope-specific CD8 +T cells promotes accumulation of extra-epitopic amino acid substitutions associated with viral resistance to these T cells. Virus Res 2024; 343:199355. [PMID: 38490580 PMCID: PMC10955411 DOI: 10.1016/j.virusres.2024.199355] [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: 01/10/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Influenza viruses are notorious for their capacity to evade host immunity. Not only can they evade recognition by virus-neutralizing antibodies, there is also evidence that they accumulate mutations in epitopes recognized by virus-specific CD8+T cells. In addition, we have shown previously that human influenza A viruses were less well recognized than avian influenza viruses by CD8+T cells directed to the highly conserved, HLA-A*02:01 restricted M158-66 epitope located in the Matrix 1 (M1) protein. Amino acid differences at residues outside the epitope were responsible for the differential recognition, and it was hypothesized that this reflected immune adaptation of human influenza viruses to selective pressure exerted by M158-66-specific CD8+T cells in the human population. In the present study, we tested this hypothesis and investigated if selective pressure exerted by M158-66 epitope-specific CD8+T cells could drive mutations at the extra-epitopic residues in vitro. To this end, isogenic influenza A viruses with the M1 gene of a human or an avian influenza virus were serially passaged in human lung epithelial A549 cells that transgenically express the HLA-A*02:01 molecule or not, in the presence or absence of M158-66 epitope-specific CD8+T cells. Especially in the virus with the M1 gene of an avian influenza virus, variants emerged with mutations at the extra-epitopic residues associated with reduced recognition by M158-66-specific T cells as detected by Next Generation Sequencing. Although the emergence of these variants was observed in the absence of selective pressure exerted by M158-66 epitope-specific CD8+T cells, their proportion was much larger in the presence of this selective pressure.
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Affiliation(s)
- Janina M Jansen
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
| | - Robert Meineke
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
| | - Antonia Molle
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Giulietta Saletti
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
| | - Guus F Rimmelzwaan
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany.
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5
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Haque A, Pant AB. The coevolution of Covid-19 and host immunity. EXPLORATION OF MEDICINE 2024:167-184. [DOI: 10.37349/emed.2024.00214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 01/05/2025] Open
Abstract
The dynamic of the virus-host interaction is subject to constant
evolution, which makes it difficult to predict when the SARS-CoV-2 pandemic
will become endemic. Vaccines in conjunction with efforts around masking and
social distancing have reduced SARS-CoV-2 infection rates, however, there
are still significant challenges to contend with before the pandemic shifts
to endemic, such as the coronavirus acquiring mutations that allow the virus
to dodge the immunity acquired by hosts. SARS-CoV-2 variants deploy
convergent evolutionary mechanisms to sharpen their ability to impede the
host’s innate immune response. The continued emergence of variants and
sub-variants poses a significant hurdle to reaching endemicity. This
underscores the importance of continued public health measures to control
SARS-CoV-2 transmission and the need to develop better second-generation
vaccines and effective treatments that would tackle current and future
variants. We hypothesize that the hosts’ immunity to the virus is also
evolving, which is likely to abet the process of reaching
endemicity.
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Affiliation(s)
- Azizul Haque
- Department of Microbiology and Immunology, Geisel School of
Medicine at Dartmouth, Lebanon, NH 03756, USA
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6
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Radwan J, Kohi C, Ejsmond M, Paganini J, Pontarotti P. Integration of the immune memory into the pathogen-driven MHC polymorphism hypothesis. HLA 2023; 102:653-659. [PMID: 37688391 DOI: 10.1111/tan.15216] [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: 02/23/2023] [Revised: 06/01/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Major histocompatibility complex (MHC) genes (referred to as human leukocyte antigen or HLA in humans) are a key component of vertebrate immune systems, coding for proteins which present antigens to T-cells. These genes are outstanding in their degree of polymorphism, with important consequences for human and animal health. The polymorphism is thought to arise from selection pressures imposed by pathogens on MHC allomorphs, which differ in their antigen-binding capacity. However, the existing theory has not considered MHC selection in relation to the formation of immune memory. In this paper, we argue that this omission limits our understanding of the evolution of MHC polymorphism and its role in disease. We review recent evidence that has emerged from the massive research effort related to the SARS-CoV-2 pandemics, and which provides new evidence for the role of MHC in shaping immune memory. We then discuss why the inclusion of immune memory within the existing theory may have non-trivial consequence for our understanding of the evolution of MHC polymorphism. Finally, we will argue that neglecting immune memory hinders our interpretation of empirical findings, and postulate that future studies focusing on pathogen-driven MHC selection would benefit from stratifying the available data according to the history of infection (and vaccination, if relevant).
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Affiliation(s)
- Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Chirine Kohi
- MEPHI, Aix Marseille Université, Marseille, France
| | - Maciej Ejsmond
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | | | - Pierre Pontarotti
- MEPHI, Aix Marseille Université, Marseille, France
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
- SNC 5039 CNRS, Marseille, France
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7
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Khadri L, Ziraksaz MH, Barekzai AB, Ghauri B. T cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 202:183-217. [PMID: 38237986 DOI: 10.1016/bs.pmbts.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a comprehensive analysis of T cell responses in COVID-19, focusing on T cell differentiation, specificity, and functional characteristics during SARS-CoV-2 infection. The differentiation of T cells in COVID-19 is explored, highlighting the key factors that influence T cell fate and effector functions. The immunology of the spike protein, a critical component of SARS-CoV-2, is discussed in detail, emphasizing its role in driving T-cell responses. The cellular immune responses against SARS-CoV-2 during acute infection are examined, including the specificity, phenotype, and functional attributes of SARS-CoV-2-specific T-cell responses. Furthermore, the chapter explores T-cell cross-recognition against other human coronaviruses (HCoVs) and the mechanisms of immune regulation mediated by spike proteins. This includes the induction of regulation through the innate immune system, the activation of self-spike protein-cross-reactive regulatory T cells, and the impact of self-tolerance on the regulation of spike proteins. The chapter investigates T cell responses to self-spike proteins and their implications in disease. The role of spike proteins as immunological targets in the context of COVID-19 is examined, shedding light on potential therapeutic interventions and clinical trials in autoimmune diseases. In conclusion, this chapter provides a comprehensive understanding of T cell responses in COVID-19, highlighting their differentiation, immune regulation, and clinical implications. This knowledge contributes to the development of targeted immunotherapies, vaccine strategies, and diagnostic approaches for COVID-19 and other related diseases.
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Affiliation(s)
- Laiqha Khadri
- Department of Biotechnology, Immune Inspired, Bangalore.
| | | | | | - Baber Ghauri
- Department of Biotechnology, Immune Inspired, Bangalore
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8
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Wong KH, Lal SK. Alternative antiviral approaches to combat influenza A virus. Virus Genes 2023; 59:25-35. [PMID: 36260242 PMCID: PMC9832087 DOI: 10.1007/s11262-022-01935-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/06/2022] [Indexed: 01/14/2023]
Abstract
Influenza A (IAV) is a major human respiratory pathogen that contributes to a significant threat to health security, worldwide. Despite vaccinations and previous immunisations through infections, humans can still be infected with influenza several times throughout their lives. This phenomenon is attributed to the antigenic changes of hemagglutinin (HA) and neuraminidase (NA) proteins in IAV via genetic mutation and reassortment, conferring antigenic drift and antigenic shift, respectively. Numerous findings indicate that slow antigenic drift and reassortment-derived antigenic shift exhibited by IAV are key processes that allow IAVs to overcome the previously acquired host immunity, which eventually leads to the annual re-emergence of seasonal influenza and even pandemic influenza, in rare occasions. As a result, current therapeutic options hit a brick wall quickly. As IAV remains a constant threat for new outbreaks worldwide, the underlying processes of genetic changes and alternative antiviral approaches for IAV should be further explored to improve disease management. In the light of the above, this review discusses the characteristics and mechanisms of mutations and reassortments that contribute to IAV's evolution. We also discuss several alternative RNA-targeting antiviral approaches, namely the CRISPR/Cas13 systems, RNA interference (RNAi), and antisense oligonucleotides (ASO) as potential antiviral approaches against IAV.
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Affiliation(s)
- Ka Heng Wong
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor DE, Malaysia.
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Selangor, Malaysia.
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9
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Chen J, Tan S, Avadhanula V, Moise L, Piedra PA, De Groot AS, Bahl J. Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Comput Biol 2023; 19:e1010360. [PMID: 36626370 PMCID: PMC9870173 DOI: 10.1371/journal.pcbi.1010360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/23/2023] [Accepted: 12/07/2022] [Indexed: 01/11/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
| | - Swan Tan
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne S. De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
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10
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Shafqat A, Omer MH, Ahmad O, Niaz M, Abdulkader HS, Shafqat S, Mushtaq AH, Shaik A, Elshaer AN, Kashir J, Alkattan K, Yaqinuddin A. SARS-CoV-2 epitopes inform future vaccination strategies. Front Immunol 2022; 13:1041185. [PMID: 36505475 PMCID: PMC9732895 DOI: 10.3389/fimmu.2022.1041185] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
All currently approved COVID-19 vaccines utilize the spike protein as their immunogen. SARS-CoV-2 variants of concern (VOCs) contain mutations in the spike protein, enabling them to escape infection- and vaccination-induced immune responses to cause reinfection. New vaccines are hence being researched intensively. Studying SARS-CoV-2 epitopes is essential for vaccine design, as identifying targets of broadly neutralizing antibody responses and immunodominant T-cell epitopes reveal candidates for inclusion in next-generation COVID-19 vaccines. We summarize the major studies which have reported on SARS-CoV-2 antibody and T-cell epitopes thus far. These results suggest that a future of pan-coronavirus vaccines, which not only protect against SARS-CoV-2 but numerous other coronaviruses, may be possible. The T-cell epitopes of SARS-CoV-2 have gotten less attention than neutralizing antibody epitopes but may provide new strategies to control SARS-CoV-2 infection. T-cells target many SARS-CoV-2 antigens other than spike, recognizing numerous epitopes within these antigens, thereby limiting the chance of immune escape by VOCs that mainly possess spike protein mutations. Therefore, augmenting vaccination-induced T-cell responses against SARS-CoV-2 may provide adequate protection despite broad antibody escape by VOCs.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,*Correspondence: Areez Shafqat,
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Omar Ahmad
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mahnoor Niaz
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | | | - Abdullah Shaik
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,Department of Comparative Medicine, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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11
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Dolton G, Rius C, Hasan MS, Wall A, Szomolay B, Behiry E, Whalley T, Southgate J, Fuller A, Morin T, Topley K, Tan LR, Goulder PJR, Spiller OB, Rizkallah PJ, Jones LC, Connor TR, Sewell AK. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 2022; 185:2936-2951.e19. [PMID: 35931021 PMCID: PMC9279490 DOI: 10.1016/j.cell.2022.07.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/08/2022] [Accepted: 07/07/2022] [Indexed: 01/06/2023]
Abstract
We studied the prevalent cytotoxic CD8 T cell response mounted against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein269-277 epitope (sequence YLQPRTFLL) via the most frequent human leukocyte antigen (HLA) class I worldwide, HLA A∗02. The Spike P272L mutation that has arisen in at least 112 different SARS-CoV-2 lineages to date, including in lineages classified as "variants of concern," was not recognized by the large CD8 T cell response seen across cohorts of HLA A∗02+ convalescent patients and individuals vaccinated against SARS-CoV-2, despite these responses comprising of over 175 different individual T cell receptors. Viral escape at prevalent T cell epitopes restricted by high frequency HLAs may be particularly problematic when vaccine immunity is focused on a single protein such as SARS-CoV-2 Spike, providing a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlighting the need for monitoring T cell escape in new SARS-CoV-2 variants.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Md Samiul Hasan
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Barbara Szomolay
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK
| | - Enas Behiry
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Thomas Whalley
- School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK
| | - Joel Southgate
- School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Katie Topley
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Li Rong Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, OX3 9DU Oxford, England, UK
| | - Owen B Spiller
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Lucy C Jones
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Centre for Clinical Research, Royal Glamorgan Hospital, Ynysmaerdy CF72 8XR, UK
| | - Thomas R Connor
- Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK; School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK; Pathogen genomics Unit, Public Health Wales NHS Trust, CF14 4XW Cardiff, Wales, UK.
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK.
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12
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [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: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- 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, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- 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, Parkville, VIC, Australia
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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13
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Abstract
The adaptive immune response is a major determinant of the clinical outcome after SARS-CoV-2 infection and underpins vaccine efficacy. T cell responses develop early and correlate with protection but are relatively impaired in severe disease and are associated with intense activation and lymphopenia. A subset of T cells primed against seasonal coronaviruses cross reacts with SARS-CoV-2 and may contribute to clinical protection, particularly in early life. T cell memory encompasses broad recognition of viral proteins, estimated at around 30 epitopes within each individual, and seems to be well sustained so far. This breadth of recognition can limit the impact of individual viral mutations and is likely to underpin protection against severe disease from viral variants, including Omicron. Current COVID-19 vaccines elicit robust T cell responses that likely contribute to remarkable protection against hospitalization or death, and novel or heterologous regimens offer the potential to further enhance cellular responses. T cell immunity plays a central role in the control of SARS-CoV-2 and its importance may have been relatively underestimated thus far.
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Affiliation(s)
- Paul Moss
- University of Birmingham, Birmingham, UK.
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14
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de Silva TI, Liu G, Lindsey BB, Dong D, Moore SC, Hsu NS, Shah D, Wellington D, Mentzer AJ, Angyal A, Brown R, Parker MD, Ying Z, Yao X, Turtle L, Dunachie S, Maini MK, Ogg G, Knight JC, Peng Y, Rowland-Jones SL, Dong T. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience 2021; 24:103353. [PMID: 34729465 PMCID: PMC8552693 DOI: 10.1016/j.isci.2021.103353] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 10/28/2022] Open
Abstract
We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.
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Affiliation(s)
- Thushan I. de Silva
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, China
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
| | - Nienyun Sharon Hsu
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
| | - Dhruv Shah
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alexander J. Mentzer
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrienn Angyal
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Rebecca Brown
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Matthew D. Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield S10 2JF, UK
| | - Zixi Ying
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
- Tropical & Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (Member of Liverpool Health Partners), Liverpool L7 8XP, UK
| | - Susanna Dunachie
- Centre For Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Mala K. Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Graham Ogg
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Julian C. Knight
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah L. Rowland-Jones
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
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15
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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16
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Schweininger J, Scherer M, Rothemund F, Schilling EM, Wörz S, Stamminger T, Muller YA. Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers. PLoS Pathog 2021; 17:e1009863. [PMID: 34370791 PMCID: PMC8376021 DOI: 10.1371/journal.ppat.1009863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023] Open
Abstract
Restriction factors are potent antiviral proteins that constitute a first line of intracellular defense by blocking viral replication and spread. During co-evolution, however, viruses have developed antagonistic proteins to modulate or degrade the restriction factors of their host. To ensure the success of lytic replication, the herpesvirus human cytomegalovirus (HCMV) expresses the immediate-early protein IE1, which acts as an antagonist of antiviral, subnuclear structures termed PML nuclear bodies (PML-NBs). IE1 interacts directly with PML, the key protein of PML-NBs, through its core domain and disrupts the dot-like multiprotein complexes thereby abrogating the antiviral effects. Here we present the crystal structures of the human and rat cytomegalovirus core domain (IE1CORE). We found that IE1CORE domains, also including the previously characterized IE1CORE of rhesus CMV, form a distinct class of proteins that are characterized by a highly similar and unique tertiary fold and quaternary assembly. This contrasts to a marked amino acid sequence diversity suggesting that strong positive selection evolved a conserved fold, while immune selection pressure may have fostered sequence divergence of IE1. At the same time, we detected specific differences in the helix arrangements of primate versus rodent IE1CORE structures. Functional characterization revealed a conserved mechanism of PML-NB disruption, however, primate and rodent IE1 proteins were only effective in cells of the natural host species but not during cross-species infection. Remarkably, we observed that expression of HCMV IE1 allows rat cytomegalovirus replication in human cells. We conclude that cytomegaloviruses have evolved a distinct protein tertiary structure of IE1 to effectively bind and inactivate an important cellular restriction factor. Furthermore, our data show that the IE1 fold has been adapted to maximize the efficacy of PML targeting in a species-specific manner and support the concept that the PML-NBs-based intrinsic defense constitutes a barrier to cross-species transmission of HCMV. Cytomegaloviruses have evolved in very close association with their hosts resulting in a highly species-specific replication. Cell-intrinsic proteins, known as restriction factors, constitute important barriers for cross-species infection of viruses. All cytomegaloviruses characterized so far express an abundant immediate-early protein, termed IE1, that binds to the cellular restriction factor promyelocytic leukemia protein (PML) and antagonizes its repressive activity on viral gene expression. Here, we present the crystal structures of the PML-binding domains of rat and human cytomegalovirus IE1. Despite low amino-acid sequence identity both proteins share a highly similar and unique fold forming a distinct protein class. Functional characterization revealed a common mechanism of PML antagonization. However, we also detected that the respective IE1 proteins only interact with PML proteins of the natural host species. Interestingly, expression of HCMV IE1 allows rat cytomegalovirus infection in human cells. This indicates that the cellular restriction factor PML forms an important barrier for cross-species infection of cytomegaloviruses that might be overcome by adaptation of IE1 protein function. Our data suggest that the cytomegalovirus IE1 structure represents an evolutionary optimized protein fold targeting PML proteins via coiled-coil interactions.
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Affiliation(s)
- Johannes Schweininger
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | | | | | - Sonja Wörz
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
- * E-mail: (TS); (YAM)
| | - Yves A. Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- * E-mail: (TS); (YAM)
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17
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Intranasal Immunization with the Influenza A Virus Encoding Truncated NS1 Protein Protects Mice from Heterologous Challenge by Restraining the Inflammatory Response in the Lungs. Microorganisms 2021; 9:microorganisms9040690. [PMID: 33810549 PMCID: PMC8067201 DOI: 10.3390/microorganisms9040690] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Influenza viruses with an impaired NS1 protein are unable to antagonize the innate immune system and, therefore, are highly immunogenic because of the self-adjuvating effect. Hence, NS1-mutated viruses are considered promising candidates for the development of live-attenuated influenza vaccines and viral vectors for intranasal administration. We investigated whether the immunogenic advantage of the virus expressing only the N-terminal half of the NS1 protein (124 a.a.) can be translated into the induction of protective immunity against a heterologous influenza virus in mice. We found that immunization with either the wild-type A/PR/8/34 (H1N1) influenza strain (A/PR8/NSfull) or its NS1-shortened counterpart (A/PR8/NS124) did not prevent the viral replication in the lungs after the challenge with the A/Aichi/2/68 (H3N2) virus. However, mice immunized with the NS1-shortened virus were better protected from lethality after the challenge with the heterologous virus. Besides showing the enhanced influenza-specific CD8+ T-cellular response in the lungs, immunization with the A/PR8/NS124 virus resulted in reduced concentrations of proinflammatory cytokines and the lower extent of leukocyte infiltration in the lungs after the challenge compared to A/PR8/NSfull or the control group. The data show that intranasal immunization with the NS1-truncated virus may better induce not only effector T-cells but also certain immunoregulatory mechanisms, reducing the severity of the innate immune response after the heterologous challenge.
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18
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Fellay J, Pedergnana V. Exploring the interactions between the human and viral genomes. Hum Genet 2019; 139:777-781. [PMID: 31729546 DOI: 10.1007/s00439-019-02089-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, genome-wide association studies led to major advances in identifying human genetic variants associated with infectious disease susceptibility. On the pathogen side, comparable methods are now applied to identify disease-modulating pathogen variants. As host and pathogen variants jointly determine disease outcomes, the most recent development has been to explore simultaneously host and pathogen genomes, through so-called genome-to-genome studies. In this review, we provide some background on the development of genome-to-genome analysis and we detail the first wave of studies in this emerging field, which focused on patients chronically infected with HIV and hepatitis C virus. We also discuss the need for novel statistical methods to better tackle the issues of population stratification and multiple testing. Finally, we speculate on future research areas where genome-to-genome analysis may prove to be particularly effective.
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Affiliation(s)
- Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Vincent Pedergnana
- French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM), Montpellier, France
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19
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Palmer DS, Turner I, Fidler S, Frater J, Goedhals D, Goulder P, Huang KHG, Oxenius A, Phillips R, Shapiro R, Vuuren CV, McLean AR, McVean G. Mapping the drivers of within-host pathogen evolution using massive data sets. Nat Commun 2019; 10:3017. [PMID: 31289267 PMCID: PMC6616926 DOI: 10.1038/s41467-019-10724-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/20/2019] [Indexed: 11/09/2022] Open
Abstract
Differences among hosts, resulting from genetic variation in the immune system or heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic association studies can potentially identify such interactions. However, extensive and correlated genetic population structure in hosts and pathogens presents a substantial risk of confounding analyses. Moreover, the multiple testing burden of interaction scanning can potentially limit power. We present a Bayesian approach for detecting host influences on pathogen evolution that exploits vast existing data sets of pathogen diversity to improve power and control for stratification. The approach models key processes, including recombination and selection, and identifies regions of the pathogen genome affected by host factors. Our simulations and empirical analysis of drug-induced selection on the HIV-1 genome show that the method recovers known associations and has superior precision-recall characteristics compared to other approaches. We build a high-resolution map of HLA-induced selection in the HIV-1 genome, identifying novel epitope-allele combinations.
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Affiliation(s)
- Duncan S Palmer
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK.
| | - Isaac Turner
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Sarah Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, W2 1PG, UK
| | - John Frater
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Dominique Goedhals
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4013, South Africa
| | - Philip Goulder
- Division of Infectious Diseases, University of the Free State, and 3 Military Hospital, Bloemfontein, 9300, South Africa
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
| | - Kuan-Hsiang Gary Huang
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Einstein Medical Center Philadelphia, 5501 Old York Road, PA, 19141, USA
| | - Annette Oxenius
- Institute of Microbiology, Swiss Federal Institute of Technology Zurich, 8093, Zurich, Switzerland
| | - Rodney Phillips
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LE, UK
- Faculty of Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, BO 320, Botswana
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02215, USA
| | - Cloete van Vuuren
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4013, South Africa
| | - Angela R McLean
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Zoology Department, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Gil McVean
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
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Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved? J Virol 2019; 93:JVI.01534-18. [PMID: 30626684 PMCID: PMC6401462 DOI: 10.1128/jvi.01534-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/26/2018] [Indexed: 01/10/2023] Open
Abstract
Universal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear how rapidly T cell-inducing vaccines will select for viruses that escape these T cell responses. Our mathematical models explore the factors that contribute to the conservation of CD8 T cell epitopes and how rapidly the virus will evolve in response to T cell-inducing vaccines. We identify the key biological parameters to be measured and questions that need to be addressed in future studies. The high degree of conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow for the development of T cell-inducing vaccines that provide protection across different strains and subtypes. This conservation is not fully explained by functional constraint, since an additional mutation(s) can compensate for the replicative fitness loss of IAV escape variants. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may have only a modest effect on transmission. Second, polymorphism of the human major histocompatibility complex class I (MHC-I) gene restricts the advantage of an escape variant to only a small fraction of the human population who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell escape variants may result in a compensatory increase in the responses to other epitopes of IAV. We use a combination of population genetics and epidemiological models to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape variants. We conclude that for a wide range of biologically reasonable parameters, the invasion of an escape variant virus will be slow, with a timescale of a decade or more. The results suggest T cell-inducing vaccines do not engender the rapid evolution of IAV. Finally, we identify key parameters whose measurement will allow for more accurate quantification of the long-term effectiveness and impact of universal T cell-inducing influenza vaccines. IMPORTANCE Universal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear how rapidly T cell-inducing vaccines will select for viruses that escape these T cell responses. Our mathematical models explore the factors that contribute to the conservation of CD8 T cell epitopes and how rapidly the virus will evolve in response to T cell-inducing vaccines. We identify the key biological parameters to be measured and questions that need to be addressed in future studies.
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21
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Voskarides K, Christaki E, Nikolopoulos GK. Influenza Virus-Host Co-evolution. A Predator-Prey Relationship? Front Immunol 2018; 9:2017. [PMID: 30245689 PMCID: PMC6137132 DOI: 10.3389/fimmu.2018.02017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza virus continues to cause yearly seasonal epidemics worldwide and periodically pandemics. Although influenza virus infection and its epidemiology have been extensively studied, a new pandemic is likely. One of the reasons influenza virus causes epidemics is its ability to constantly antigenically transform through genetic diversification. However, host immune defense mechanisms also have the potential to evolve during short or longer periods of evolutionary time. In this mini-review, we describe the evolutionary procedures related with influenza viruses and their hosts, under the prism of a predator-prey relationship.
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Textor J, Fähnrich A, Meinhardt M, Tune C, Klein S, Pagel R, König P, Kalies K, Westermann J. Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response. THE JOURNAL OF IMMUNOLOGY 2018; 201:350-358. [PMID: 29884700 DOI: 10.4049/jimmunol.1800091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/19/2018] [Indexed: 11/19/2022]
Abstract
Immunological differences between hosts, such as diverse TCR repertoires, are widely credited for reducing the risk of pathogen spread and adaptation in a population. Within-host immunological diversity might likewise be important for robust pathogen control, but to what extent naive TCR repertoires differ across different locations in the same host is unclear. T cell zones (TCZs) in secondary lymphoid organs provide secluded microenvironmental niches. By harboring distinct TCRs, such niches could enhance within-host immunological diversity. In contrast, rapid T cell migration is expected to dilute such diversity. In this study, we combined tissue microdissection and deep sequencing of the TCR β-chain to examine the extent to which TCR repertoires differ between TCZs in murine spleens. In the absence of Ag, we found little evidence for differences between TCZs of the same spleen. Yet, 3 d after immunization with sheep RBCs, we observed a >10-fold rise in the number of clones that appeared to localize to individual zones. Remarkably, these differences largely disappeared at 4 d after immunization, when hallmarks of an ongoing immune response were still observed. These data suggest that in the absence of Ag, any repertoire differences observed between TCZs of the same host can largely be attributed to random clone distribution. Upon Ag challenge, TCR repertoires in TCZs first segregate and then homogenize within days. Such "transient mosaic" dynamics could be an important barrier for pathogen adaptation and spread during an immune response.
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Affiliation(s)
- Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; and
| | - Anke Fähnrich
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Martin Meinhardt
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Cornelia Tune
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Sebastian Klein
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Rene Pagel
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Peter König
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Kathrin Kalies
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Jürgen Westermann
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
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23
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Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci 2017; 18:ijms18081650. [PMID: 28783091 PMCID: PMC5578040 DOI: 10.3390/ijms18081650] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves.
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