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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [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: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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2
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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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3
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Morshedi F, Nazeri E, Saleh M, Farahmand B. Fusion Protein Consisting of Hemagglutinin Small Subunit and Truncated Nucleoprotein as a Universal Influenza Vaccine Candidate: Starting In-Silico Evaluation Toward In Vitro Expression. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2023; 15:57-62. [PMID: 37313538 PMCID: PMC10259740 DOI: 10.4103/jpbs.jpbs_114_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/29/2018] [Accepted: 09/11/2019] [Indexed: 06/15/2023] Open
Abstract
Background Influenza virus is a respiratory pathogen, which causes high degree of mortality and morbidity during seasonal epidemics and sporadic pandemics. By selecting conserved antigenic proteins, for example, hemagglutinin small subunit (HA2) and nucleoprotein (NP), we aimed to develop a vaccine based on a fusion protein leading to both cellular and humoral responses that are the most challenging aspects in designing a universal vaccine. Materials and Methods The bioinformatics analysis was performed for HA2-NP structure and function prediction. Primers for the antigenic part of NP were designed using bioinformatics tools. The desired product was amplified via polymerase chain reaction using the designed primers, which was then penetrated into T vector, followed by insertion into pET28a vector in order to construct pET28a/NP. The pET28a/HA2, previously generated in our lab, was digested with the same restriction enzymes as pET28a/NP (HindIII/Xhol). Then, NP was inserted to the downstream region of HA2 to construct pET28a/HA2. Results The generated pET28a/HA2-NP was transformed into Escherichia coli BL21 (DE3). The expression was induced by isopropyl β-d-l-thiogalactopyranoside. The results showed that the antigenic segment of NP was successfully cloned into pET28a/ HA2. The protein band of HA2-NP was observed on sodium dodecyl sulfate polyacrylamide gel electrophoresis, confirmed by Western blotting and purified with Ni-NTA purification system (QIAGEN, Germany). Conclusion As currently available vaccines can cause some allergic reactions, using a chimer protein based on the bioinformatics analysis is continual, safe, and affordable, thus stimulating both cellular and humoral immunity systems. Our construct could potentially provide a basis for a universal vaccine candidate.
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Affiliation(s)
- Fatemeh Morshedi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
- Faculty of Sciences, Azad University, Tehran, Iran
| | - Elaheh Nazeri
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Saleh
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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4
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Nguyen AT, Lau HMP, Sloane H, Jayasinghe D, Mifsud NA, Chatzileontiadou DSM, Grant EJ, Szeto C, Gras S. Homologous peptides derived from influenza A, B and C viruses induce variable CD8 + T cell responses with cross-reactive potential. Clin Transl Immunology 2022; 11:e1422. [PMID: 36275878 PMCID: PMC9581725 DOI: 10.1002/cti2.1422] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Objective Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally, infecting humans and causing widespread morbidity and mortality. Here, we investigate the T cell response towards an immunodominant IAV epitope, NP265‐273, and its IBV and ICV homologues, presented by HLA‐A*03:01 molecule expressed in ~ 4% of the global population (~ 300 million people). Methods We assessed the magnitude (tetramer staining) and quality of the CD8+ T cell response (intracellular cytokine staining) towards NP265‐IAV and described the T cell receptor (TCR) repertoire used to recognise this immunodominant epitope. We next assessed the immunogenicity of NP265‐IAV homologue peptides from IBV and ICV and the ability of CD8+ T cells to cross‐react towards these homologous peptides. Furthermore, we determined the structures of NP265‐IAV and NP323‐IBV peptides in complex with HLA‐A*03:01 by X‐ray crystallography. Results Our study provides a detailed characterisation of the CD8+ T cell response towards NP265‐IAV and its IBV and ICV homologues. The data revealed a diverse repertoire for NP265‐IAV that is associated with superior anti‐viral protection. Evidence of cross‐reactivity between the three different influenza virus strain‐derived epitopes was observed, indicating the discovery of a potential vaccination target that is broad enough to cover all three influenza strains. Conclusion We show that while there is a potential to cross‐protect against distinct influenza virus lineages, the T cell response was stronger against the IAV peptide than IBV or ICV, which is an important consideration when choosing targets for future vaccine design.
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Affiliation(s)
- Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Hiu Ming Peter Lau
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Demetra SM Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Emma J Grant
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
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5
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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] [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
- *Correspondence: Katherine Kedzierska,
| | - 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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6
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Bull MB, Gu H, Ma FNL, Perera LP, Poon LLM, Valkenburg SA. Next-generation T cell-activating vaccination increases influenza virus mutation prevalence. SCIENCE ADVANCES 2022; 8:eabl5209. [PMID: 35385318 PMCID: PMC8986104 DOI: 10.1126/sciadv.abl5209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To determine the potential for viral adaptation to T cell responses, we probed the full influenza virus genome by next-generation sequencing directly ex vivo from infected mice, in the context of an experimental T cell-based vaccine, an H5N1-based viral vectored vaccinia vaccine Wyeth/IL-15/5Flu, versus the current standard-of-care, seasonal inactivated influenza vaccine (IIV) and unvaccinated conditions. Wyeth/IL-15/5Flu vaccination was coincident with increased mutation incidence and frequency across the influenza genome; however, mutations were not enriched within T cell epitope regions, but high allele frequency mutations within conserved hemagglutinin stem regions and PB2 mammalian adaptive mutations arose. Depletion of CD4+ and CD8+ T cell subsets led to reduced frequency of mutants in vaccinated mice; therefore, vaccine-mediated T cell responses were important drivers of virus diversification. Our findings suggest that Wyeth/IL-15/5Flu does not generate T cell escape mutants but increases stochastic events for virus adaptation by stringent bottlenecks.
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Affiliation(s)
- Maireid B. Bull
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fionn N. L. Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyanage P. Perera
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1374, USA
| | - Leo L. M. Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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7
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Zhao S, Lou J, Cao L, Zheng H, Chong MKC, Chen Z, Chan RWY, Zee BCY, Chan PKS, Wang MH. Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. BMC Infect Dis 2021; 21:1039. [PMID: 34620109 PMCID: PMC8495436 DOI: 10.1186/s12879-021-06729-w] [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: 05/07/2021] [Accepted: 09/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. Characterizing the role of the mutation activities is of importance to understand how the evolution of pathogen shapes the epidemiological outcomes at population scale. METHODS We developed a statistical framework to reconstruct variant-specific reproduction numbers and estimate transmission advantage associated with the mutation activities marked by single substitution empirically. Using likelihood-based approach, the model is exemplified with the COVID-19 surveillance data from January 1 to June 30, 2020 in California, USA. We explore the potential of this framework to generate early warning signals for detecting transmission advantage on a real-time basis. RESULTS The modelling framework in this study links together the mutation activity at molecular scale and COVID-19 transmissibility at population scale. We find a significant transmission advantage of COVID-19 associated with the D614G substitution, which increases the infectivity by 54% (95%CI: 36, 72). For the early alarming potentials, the analytical framework is demonstrated to detect this transmission advantage, before the mutation reaches dominance, on a real-time basis. CONCLUSIONS We reported an evidence of transmission advantage associated with D614G substitution, and highlighted the real-time estimating potentials of modelling framework.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Hong Zheng
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Marc K. C. Chong
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Zigui Chen
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, China
| | - Renee W. Y. Chan
- Department of Paediatrics, Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- CUHK-UMCU Joint Research Laboratory of Respiratory Virus & Immunobiology, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Benny C. Y. Zee
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Paul K. S. Chan
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, China
| | - Maggie H. Wang
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
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8
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Zhao S, Ran J, Han L. Exploring the Interaction between E484K and N501Y Substitutions of SARS-CoV-2 in Shaping the Transmission Advantage of COVID-19 in Brazil: A Modeling Study. Am J Trop Med Hyg 2021; 105:1247-1254. [PMID: 34583340 PMCID: PMC8592180 DOI: 10.4269/ajtmh.21-0412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes is one of the major challenges of disease control. Considering the growth of epidemic curve and the circulating SARS-CoV-2 variants in Brazil, the role of locally prevalent E484K and N501Y substitutions in contributing to the epidemiological outcomes is of public health interest for investigation. We developed a likelihood-based statistical framework to reconstruct reproduction numbers, estimate transmission advantage associated with different SARS-CoV-2 variants regarding the marking (identifying) 484K and 501Y substitutions (including Alpha, Zeta, and Gamma variants) in Brazil, and explored the interactive effects of genetic activities on transmission advantage marked by these two mutations. We found a significant transmission advantage associated with the 484K/501Y variants (including P.1 or Gamma variants), which increased the infectivity significantly by 23%. In contrast and by comparison to Gamma variants, E484K or N501Y (including Alpha or Zeta variants) substitution alone appeared less likely to secure a concrete transmission advantage in Brazil. Our finding indicates that the combined impact of genetic activities on transmission advantage marked by 484K/501Y outperforms their independent contributions in Brazil, which implies an interactive effect in shaping the increase in the infectivity of COVID-19. Future studies are needed to investigate the mechanisms of how E484K and N501Y mutations and the complex genetic mutation activities marked by them in SARS-CoV-2 affect the transmissibility of COVID-19.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Jinjun Ran
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lefei Han
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Toward a universal influenza virus vaccine: Some cytokines may fulfill the request. Cytokine 2021; 148:155703. [PMID: 34555604 DOI: 10.1016/j.cyto.2021.155703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 01/21/2023]
Abstract
The influenza virus annually causes widespread damages to the health and economy of the global community. Vaccination is currently the most crucial strategy in reducing the number of patients. Genetic variations, the high diversity of pandemic viruses, and zoonoses make it challenging to select suitable strains for annual vaccine production. If new pandemic viruses emerge, it will take a long time to produce a vaccine according to the new strains. In the present study, intending to develop a universal influenza vaccine, new bicistronic DNA vaccines were developed that expressed NP or NPm antigen with one of modified IL-18/ IL-17A/ IL-22 cytokine adjuvants. NPm is a mutant form of the antigen that has the ability for cytoplasmic accumulation. In order to investigate and differentiate the role of each of the components of Th1, Th2, Th17, and Treg cellular immune systems in the performance of vaccines, Treg competent and Treg suppressed mouse groups were used. Mice were vaccinated with Foxp3-FC immunogen to produce Treg suppressed mouse groups. The potential of the vaccines to stimulate the immune system was assessed by IFN-γ/IL-17A Dual FluoroSpot. The vaccine's ability to induce humoral immune response was determined by measuring IgG1, IgG2a, and IgA-specific antibodies against the antigen. Kinetics of Th1, Th2, and Th17 cellular immune responses after vaccination, were assessed by evaluating the expression changes of IL-17A, IFN-γ, IL-18, IL-22, IL-4, and IL-2 cytokines by semi-quantitative real-time RT-PCR. To assess the vaccines' ability to induce heterosubtypic immunity, challenge tests with homologous and heterologous viruses were performed and then the virus titer was measured in the lungs of animals. Evaluation of the data obtained from this study showed that the DNA-vaccines coding NPm have more ability to induces a potent cross-cellular immune response and protective immunity than DNA-vaccines coding NP. Although the use of IL-18/ IL-17A/ IL-22 genetic adjuvants enhanced immune responses and protective immunity, Administration of NPm in combination with modified IL-18 (Igk-mIL18-IgFC) induced the most effective immunity in Treg competent mice group.
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10
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Bull MB, Cohen CA, Leung NH, Valkenburg SA. Universally Immune: How Infection Permissive Next Generation Influenza Vaccines May Affect Population Immunity and Viral Spread. Viruses 2021; 13:1779. [PMID: 34578360 PMCID: PMC8472936 DOI: 10.3390/v13091779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Next generation influenza vaccines that target conserved epitopes are becoming a clinical reality but still have challenges to overcome. Universal next generation vaccines are considered a vital tool to combat future pandemic viruses and have the potential to vastly improve long-term protection against seasonal influenza viruses. Key vaccine strategies include HA-stem and T cell activating vaccines; however, they could have unintended effects for virus adaptation as they recognise the virus after cell entry and do not directly block infection. This may lead to immune pressure on residual viruses. The potential for immune escape is already evident, for both the HA stem and T cell epitopes, and mosaic approaches for pre-emptive immune priming may be needed to circumvent key variants. Live attenuated influenza vaccines have not been immunogenic enough to boost T cells in adults with established prior immunity. Therefore, viral vectors or peptide approaches are key to harnessing T cell responses. A plethora of viral vector vaccines and routes of administration may be needed for next generation vaccine strategies that require repeated long-term administration to overcome vector immunity and increase our arsenal against diverse influenza viruses.
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Affiliation(s)
- Maireid B. Bull
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - Carolyn A. Cohen
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - Nancy H.L. Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, China;
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
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11
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Han AX, Felix Garza ZC, Welkers MRA, Vigeveno RM, Tran ND, Le TQM, Pham Quang T, Dang DT, Tran TNA, Ha MT, Nguyen TH, Le QT, Le TH, Hoang TBN, Chokephaibulkit K, Puthavathana P, Nguyen VVC, Nghiem MN, Nguyen VK, Dao TT, Tran TH, Wertheim HFL, Horby PW, Fox A, van Doorn HR, Eggink D, de Jong MD, Russell CA. Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children. eLife 2021; 10:e68917. [PMID: 34342576 PMCID: PMC8382297 DOI: 10.7554/elife.68917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/02/2021] [Indexed: 01/14/2023] Open
Abstract
The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analyzed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titers decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Zandra C Felix Garza
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Matthijs RA Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - René M Vigeveno
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Nhu Duong Tran
- National Institute of Hygiene and EpidemiologyHanoiViet Nam
| | | | | | | | | | | | | | | | - Thanh Hai Le
- Vietnam National Children's HospitalHanoiViet Nam
| | | | | | | | | | | | | | | | - Tinh Hien Tran
- Siriraj Hospital, Mahidol UniversityBangkokThailand
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
| | - Heiman FL Wertheim
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
- Radboud Medical Centre, Radboud UniversityNijmegenNetherlands
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Peter W Horby
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Annette Fox
- Oxford University Clinical Research UnitHanoiViet Nam
- Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- WHO Collaborating Centre for Reference and Research on InfluenzaMelbourneAustralia
| | - H Rogier van Doorn
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Dirk Eggink
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the EnvironmentBilthovenNetherlands
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
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12
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Zhao S, Lou J, Chong MKC, Cao L, Zheng H, Chen Z, Chan RWY, Zee BCY, Chan PKS, Wang MH. Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Viruses 2021; 13:638. [PMID: 33918060 PMCID: PMC8070306 DOI: 10.3390/v13040638] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023] Open
Abstract
As COVID-19 is posing a serious threat to global health, the emerging mutation in SARS-CoV-2 genomes, for example, N501Y substitution, is one of the major challenges against control of the pandemic. Characterizing the relationship between mutation activities and the risk of severe clinical outcomes is of public health importance for informing the healthcare decision-making process. Using a likelihood-based approach, we developed a statistical framework to reconstruct a time-varying and variant-specific case fatality ratio (CFR), and to estimate changes in CFR associated with a single mutation empirically. For illustration, the statistical framework is implemented to the COVID-19 surveillance data in the United Kingdom (UK). The reconstructed instantaneous CFR gradually increased from 1.0% in September to 2.2% in November 2020 and stabilized at this level thereafter, which monitors the mortality risk of COVID-19 on a real-time basis. We identified a link between the SARS-CoV-2 mutation activity at molecular scale and COVID-19 mortality risk at population scale, and found that the 501Y variants may slightly but not significantly increase 18% of fatality risk than the preceding 501N variants. We found no statistically significant evidence of change in COVID-19 mortality risk associated with 501Y variants, and highlighted the real-time estimating potentials of the modelling framework.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
- CUHK Shenzhen Research Institute, Shenzhen 518000, China
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
| | - Marc K. C. Chong
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
- CUHK Shenzhen Research Institute, Shenzhen 518000, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
- CUHK Shenzhen Research Institute, Shenzhen 518000, China
| | - Hong Zheng
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
| | - Zigui Chen
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (P.K.S.C.)
| | - Renee W. Y. Chan
- Department of Pediatrics, Chinese University of Hong Kong, Hong Kong, China;
- Hong Kong Hub of Pediatric Excellence, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- CUHK-UMCU Joint Research Laboratory of Respiratory Virus & Immunobiology, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Benny C. Y. Zee
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
- CUHK Shenzhen Research Institute, Shenzhen 518000, China
| | - Paul K. S. Chan
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (P.K.S.C.)
| | - Maggie H. Wang
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China; (J.L.); (M.K.C.C.); (L.C.); (H.Z.); (B.C.Y.Z.)
- CUHK Shenzhen Research Institute, Shenzhen 518000, China
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13
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Guo E, Guo H. CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. PLoS One 2020; 15:e0239566. [PMID: 33301503 PMCID: PMC7728258 DOI: 10.1371/journal.pone.0239566] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/23/2020] [Indexed: 01/10/2023] Open
Abstract
The ongoing pandemic of SARS-CoV-2 has brought tremendous crisis on global health care systems and industrial operations that dramatically affect the economic and social life of numerous individuals worldwide. Understanding anti-SARS-CoV-2 immune responses in population with different genetic backgrounds and tracking the viral evolution are crucial for successful vaccine design. In this study, we reported the generation of CD8 T cell epitopes by a total of 80 alleles of three major class I HLAs using NetMHC 4.0 algorithm for the SARS-CoV-2 spike protein, which can be targeted by both B cells and T cells. We found diverse capacities of S protein specific epitope presentation by different HLA alleles with very limited number of predicted epitopes for HLA-B*2705, HLA-B*4402 and HLA-B*4403 and as high as 132 epitopes for HLA-A*6601. Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed. Finally, our multiple alignment analysis indicated the absence of seasonal CoV induced cross-reactive CD8 T cells to drive these mutations. Our findings suggested that individuals with certain HLA alleles, such as B*44 are more prone to SARS-CoV-2 infection. Studying anti-S protein specific CD8 T cell immunity in diverse genetic background is critical for better control and prevention of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Elisa Guo
- Mounds View High School, Arden Hills, Minnesota, United States of America
| | - Hailong Guo
- Independent Scientist, St Paul, Minnesota, United States of America
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14
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van de Sandt CE, Clemens EB, Grant EJ, Rowntree LC, Sant S, Halim H, Crowe J, Cheng AC, Kotsimbos TC, Richards M, Miller A, Tong SYC, Rossjohn J, Nguyen THO, Gras S, Chen W, Kedzierska K. Challenging immunodominance of influenza-specific CD8 + T cell responses restricted by the risk-associated HLA-A*68:01 allomorph. Nat Commun 2019; 10:5579. [PMID: 31811120 PMCID: PMC6898063 DOI: 10.1038/s41467-019-13346-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
Although influenza viruses lead to severe illness in high-risk populations, host genetic factors associated with severe disease are largely unknown. As the HLA-A*68:01 allele can be linked to severe pandemic 2009-H1N1 disease, we investigate a potential impairment of HLA-A*68:01-restricted CD8+ T cells to mount robust responses. We elucidate the HLA-A*68:01+CD8+ T cell response directed toward an extended influenza-derived nucleoprotein (NP) peptide and show that only ~35% individuals have immunodominant A68/NP145+CD8+ T cell responses. Dissecting A68/NP145+CD8+ T cells in low vs. medium/high responders reveals that high responding donors have A68/NP145+CD8+ memory T cells with clonally expanded TCRαβs, while low-responders display A68/NP145+CD8+ T cells with predominantly naïve phenotypes and non-expanded TCRαβs. Single-cell index sorting and TCRαβ analyses link expansion of A68/NP145+CD8+ T cells to their memory potential. Our study demonstrates the immunodominance potential of influenza-specific CD8+ T cells presented by a risk HLA-A*68:01 molecule and advocates for priming CD8+ T cell compartments in HLA-A*68:01-expressing individuals for establishment of pre-existing protective memory T cell pools.
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Affiliation(s)
- C E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX, Amsterdam, Netherlands
| | - E B Clemens
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia
| | - E J Grant
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Infection and Immunity Program, Monash University, Clayton, VIC, 3800, Australia
| | - L C Rowntree
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia
| | - S Sant
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia
| | - H Halim
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - J Crowe
- Deepdene Surgery, Deepdene, VIC, 3103, Australia
| | - A C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia.,Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, VIC, 3004, Australia
| | - T C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, 3004, Australia.,Department of Medicine, Monash University, Central Clinical School, The Alfred Hospital, Melbourne, VIC, 3004, Australia
| | - M Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, 3050, Australia
| | - A Miller
- Indigenous Research Network, Griffith University, Brisbane, QLD, 4222, Australia.,Office of Indigenous Engagement, CQUniversity, Townsvillle, QLD, Australia
| | - S Y C Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, 3050, Australia.,Menzies School of Health Research, Charles Darwin University, Darwin, NT, 0811, Australia
| | - J Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - T H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia
| | - S Gras
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - W Chen
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - K Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia.
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15
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Elbahesh H, Saletti G, Gerlach T, Rimmelzwaan GF. Broadly protective influenza vaccines: design and production platforms. Curr Opin Virol 2019; 34:1-9. [DOI: 10.1016/j.coviro.2018.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023]
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16
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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: 2.8] [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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17
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Sant S, Grzelak L, Wang Z, Pizzolla A, Koutsakos M, Crowe J, Loudovaris T, Mannering SI, Westall GP, Wakim LM, Rossjohn J, Gras S, Richards M, Xu J, Thomas PG, Loh L, Nguyen THO, Kedzierska K. Single-Cell Approach to Influenza-Specific CD8 + T Cell Receptor Repertoires Across Different Age Groups, Tissues, and Following Influenza Virus Infection. Front Immunol 2018; 9:1453. [PMID: 29997621 PMCID: PMC6030351 DOI: 10.3389/fimmu.2018.01453] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells recognizing antigenic peptides derived from conserved internal viral proteins confer broad protection against distinct influenza viruses. As memory CD8+ T cells change throughout the human lifetime and across tissue compartments, we investigated how T cell receptor (TCR) composition and diversity relate to memory CD8+ T cells across anatomical sites and immunological phases of human life. We used ex vivo peptide-HLA tetramer magnetic enrichment, single-cell multiplex RT-PCR for both the TCR-alpha (TCRα) and TCR-beta (TCRβ) chains, and new TCRdist and grouping of lymphocyte interactions by paratope hotspots (GLIPH) algorithms to compare TCRs directed against the most prominent human influenza epitope, HLA-A*02:01-M158–66 (A2+M158). We dissected memory TCR repertoires directed toward A2+M158 CD8+ T cells within human tissues and compared them to human peripheral blood of young and elderly adults. Furthermore, we compared these memory CD8+ T cell repertoires to A2+M158 CD8+ TCRs during acute influenza disease in patients hospitalized with avian A/H7N9 virus. Our study provides the first ex vivo comparative analysis of paired antigen-specific TCR-α/β clonotypes across different tissues and peripheral blood across different age groups. We show that human A2+M158 CD8+ T cells can be readily detected in human lungs, spleens, and lymph nodes, and that tissue A2+M158 TCRαβ repertoires reflect A2+M158 TCRαβ clonotypes derived from peripheral blood in healthy adults and influenza-infected patients. A2+M158 TCRαβ repertoires displayed distinct features only in elderly adults, with large private TCRαβ clonotypes replacing the prominent and public TRBV19/TRAV27 TCRs. Our study provides novel findings on influenza-specific TCRαβ repertoires within human tissues, raises the question of how we can prevent the loss of optimal TCRαβ signatures with aging, and provides important insights into the rational design of T cell-mediated vaccines and immunotherapies.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,École Normale Supérieure Paris-Saclay, Université Paris-Saclay, Cachan, France
| | - Zhongfang Wang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Angela Pizzolla
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,School of Medicine, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Michael Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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18
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Variation at Extra-epitopic Amino Acid Residues Influences Suppression of Influenza Virus Replication by M1 58-66 Epitope-Specific CD8 + T Lymphocytes. J Virol 2018; 92:JVI.00232-18. [PMID: 29593036 DOI: 10.1128/jvi.00232-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/19/2018] [Indexed: 01/05/2023] Open
Abstract
Influenza virus-specific CD8+ T lymphocytes (CTLs) contribute to clearance of influenza virus infections and reduce disease severity. Variation at amino acid residues located in or outside CTL epitopes has been shown to affect viral recognition by virus-specific CTLs. In the present study, we investigated the effect of naturally occurring variation at residues outside the conserved immunodominant and HLA*0201-restricted M158-66 epitope, located in the influenza virus M1 protein, on the extent of virus replication in the presence of CTLs specific for the epitope. To this end, we used isogenic viruses with an M1 gene segment derived from either an avian or a human influenza virus, HLA-transgenic human epithelial cells, human T cell clones specific for the M158-66 epitope or a control epitope, and a novel, purposely developed in vitro system to coculture influenza virus-infected cells with T cells. We found that the M gene segment of a human influenza A/H3N2 virus afforded the virus the capacity to replicate better in the presence of M158-66-specific CTLs than the M gene segment of avian viruses. These findings are in concordance with previously observed differential CTL activation, caused by variation at extra-epitopic residues, and may reflect an immune adaptation strategy of human influenza viruses that allows them to cope with potent CTL immunity to the M158-66 epitope in HLA-A*0201-positive individuals, resulting in increased virus replication and shedding and possibly increasing disease severity.IMPORTANCE Influenza viruses are among the leading causes of acute respiratory tract infections. CD8+ T lymphocytes display a high degree of cross-reactivity with influenza A viruses of various subtypes and are considered an important correlate of protection. Unraveling viral immune evasion strategies and identifying signs of immune adaptation are important for defining the role of CD8+ T lymphocytes in affording protection more accurately. Improving our insight into the interaction between influenza viruses and virus-specific CD8+ T lymphocyte immunity may help to advance our understanding of influenza virus epidemiology, aid in risk assessment of potentially pandemic influenza virus strains, and benefit the design of vaccines that induce more broadly protective immunity.
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19
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Clemens EB, van de Sandt C, Wong SS, Wakim LM, Valkenburg SA. Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine. Vaccines (Basel) 2018; 6:vaccines6020018. [PMID: 29587436 PMCID: PMC6027237 DOI: 10.3390/vaccines6020018] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Next-generation vaccines that utilize T cells could potentially overcome the limitations of current influenza vaccines that rely on antibodies to provide narrow subtype-specific protection and are prone to antigenic mismatch with circulating strains. Evidence from animal models shows that T cells can provide heterosubtypic protection and are crucial for immune control of influenza virus infections. This has provided hope for the design of a universal vaccine able to prime against diverse influenza virus strains and subtypes. However, multiple hurdles exist for the realisation of a universal T cell vaccine. Overall primary concerns are: extrapolating human clinical studies, seeding durable effective T cell resident memory (Trm), population human leucocyte antigen (HLA) coverage, and the potential for T cell-mediated immune escape. Further comprehensive human clinical data is needed during natural infection to validate the protective role T cells play during infection in the absence of antibodies. Furthermore, fundamental questions still exist regarding the site, longevity and duration, quantity, and phenotype of T cells needed for optimal protection. Standardised experimental methods, and eventually simplified commercial assays, to assess peripheral influenza-specific T cell responses are needed for larger-scale clinical studies of T cells as a correlate of protection against influenza infection. The design and implementation of a T cell-inducing vaccine will require a consensus on the level of protection acceptable in the community, which may not provide sterilizing immunity but could protect the individual from severe disease, reduce the length of infection, and potentially reduce transmission in the community. Therefore, increasing the standard of care potentially offered by T cell vaccines should be considered in the context of pandemic preparedness and zoonotic infections, and in combination with improved antibody vaccine targeting methods. Current pandemic vaccine preparedness measures and ongoing clinical trials under-utilise T cell-inducing vaccines, reflecting the myriad questions that remain about how, when, where, and which T cells are needed to fight influenza virus infection. This review aims to bring together basic fundamentals of T cell biology with human clinical data, which need to be considered for the implementation of a universal vaccine against influenza that harnesses the power of T cells.
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Affiliation(s)
- E Bridie Clemens
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Carolien van de Sandt
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Sook San Wong
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Linda M Wakim
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Sophie A Valkenburg
- HKU Pasteur Research Pole, School of Public Health, University of Hong Kong, Hong Kong 999077, China.
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20
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Innate and adaptive T cells in influenza disease. Front Med 2018; 12:34-47. [DOI: 10.1007/s11684-017-0606-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/24/2017] [Indexed: 12/25/2022]
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21
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Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition. Sci Rep 2016; 6:33334. [PMID: 27629812 PMCID: PMC5024124 DOI: 10.1038/srep33334] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/23/2016] [Indexed: 11/24/2022] Open
Abstract
The evolutionary adaptation of the influenza A virus (IAV) to human antibodies is well characterised. Much less is known about the long-term evolution of cytotoxic T lymphocyte (CTL) epitopes, which are important antigens for clearance of infection. We construct an antigenic map of IAVs of all human subtypes using a compendium of 142 confirmed CTL epitopes, and show that IAV evolved gradually in the period 1932–2015, with infrequent antigenic jumps in the H3N2 subtype. Intriguingly, the number of CTL epitopes per virus decreases with more than one epitope per three years in the H3N2 subtype (from 84 epitopes per virus in 1968 to 64 in 2015), mostly attributed to the loss of HLA-B epitopes. We confirm these observations with epitope predictions. Our findings indicate that selection pressures imposed by CTL immunity shape the long-term evolution of IAV.
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Chai N, Swem LR, Reichelt M, Chen-Harris H, Luis E, Park S, Fouts A, Lupardus P, Wu TD, Li O, McBride J, Lawrence M, Xu M, Tan MW. Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. PLoS Pathog 2016; 12:e1005702. [PMID: 27351973 PMCID: PMC4924800 DOI: 10.1371/journal.ppat.1005702] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022] Open
Abstract
Broadly neutralizing antibodies targeting the stalk region of influenza A virus (IAV) hemagglutinin (HA) are effective in blocking virus infection both in vitro and in vivo. The highly conserved epitopes recognized by these antibodies are critical for the membrane fusion function of HA and therefore less likely to be permissive for virus mutational escape. Here we report three resistant viruses of the A/Perth/16/2009 strain that were selected in the presence of a broadly neutralizing stalk-binding antibody. The three resistant viruses harbor three different mutations in the HA stalk: (1) Gln387Lys; (2) Asp391Tyr; (3) Asp391Gly. The Gln387Lys mutation completely abolishes binding of the antibody to the HA stalk epitope. The other two mutations, Asp391Tyr and Asp391Gly, do not affect antibody binding at neutral pH and only slightly reduce binding at low pH. Interestingly, they enhance the fusion ability of the HA, representing a novel mechanism that allows productive membrane fusion even in the presence of antibody and hence virus escape from antibody neutralization. Therefore, these mutations illustrate two different resistance mechanisms used by IAV to escape broadly neutralizing stalk-binding antibodies. Compared to the wild type virus, the resistant viruses release fewer progeny viral particles during replication and are more sensitive to Tamiflu, suggesting reduced viral fitness. IAV causes seasonal epidemics and periodic pandemics that result in significant morbidity and mortality worldwide. The effectiveness of influenza vaccines is highly variable because the virus evolves rapidly and causes antibody mismatch. The use of neuraminidase inhibitors, the current standard of treatment for IAV infection, is limited by their lack of efficacy beyond 48 hours of symptom onset and by the emergence of drug resistant viruses. Recently, broadly neutralizing antibodies targeting the conserved stalk region of IAV HA have been discovered. These antibodies are able to block the infection of many or even all IAV strains, and hold great promise as the next generation of anti-flu treatment. Nonetheless, virus resistance to these antibodies has not been thoroughly studied despite the common view that broadly neutralizing stalk-binding antibodies are less permissive for mutational escape due to the functional importance of their highly conserved epitopes. In this study, we isolated three resistant viruses to a stalk-binding antibody that was previously shown to neutralize all IAV tested. Interestingly, they use two distinct mechanisms to escape the antibody, abolishing antibody binding or enhancing membrane fusion. Our study emphasizes the need to consider novel escape mechanisms when studying virus resistance to broadly neutralizing stalk-binding antibodies.
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Affiliation(s)
- Ning Chai
- Infectious Diseases Department, Genentech, South San Francisco, California, United States of America
- * E-mail: (NC); (MWT)
| | - Lee R. Swem
- Infectious Diseases Department, Genentech, South San Francisco, California, United States of America
| | - Mike Reichelt
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Haiyin Chen-Harris
- Bioinformatics & Computational Biology Department, Genentech, South San Francisco, California, United States of America
- Cancer Immunology Department, Genentech, South San Francisco, California, United States of America
| | - Elizabeth Luis
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Summer Park
- Translational Immunology Department, Genentech, South San Francisco, California, United States of America
| | - Ashley Fouts
- Infectious Diseases Department, Genentech, South San Francisco, California, United States of America
| | - Patrick Lupardus
- Structural Biology Department, Genentech, South San Francisco, California, United States of America
| | - Thomas D. Wu
- Bioinformatics & Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Olga Li
- Development Sciences Department, Genentech, South San Francisco, California, United States of America
| | - Jacqueline McBride
- Development Sciences Department, Genentech, South San Francisco, California, United States of America
| | - Michael Lawrence
- Bioinformatics & Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Min Xu
- Translational Immunology Department, Genentech, South San Francisco, California, United States of America
| | - Man-Wah Tan
- Infectious Diseases Department, Genentech, South San Francisco, California, United States of America
- * E-mail: (NC); (MWT)
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Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses. Proc Natl Acad Sci U S A 2016; 113:4440-5. [PMID: 27036003 DOI: 10.1073/pnas.1603106113] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Memory CD8(+)T lymphocytes (CTLs) specific for antigenic peptides derived from internal viral proteins confer broad protection against distinct strains of influenza A virus (IAV). However, immune efficacy can be undermined by the emergence of escape mutants. To determine how T-cell receptor (TCR) composition relates to IAV epitope variability, we used ex vivo peptide-HLA tetramer enrichment and single-cell multiplex analysis to compare TCRs targeted to the largely conserved HLA-A*0201-M158and the hypervariable HLA-B*3501-NP418antigens. The TCRαβs for HLA-B*3501-NP418 (+)CTLs varied among individuals and across IAV strains, indicating that a range of mutated peptides will prime different NP418-specific CTL sets. Conversely, a dominant public TRAV27/TRBV19(+)TCRαβ was selected in HLA-A*0201(+)donors responding to M158 This public TCR cross-recognized naturally occurring M158variants complexed with HLA-A*0201. Ternary structures showed that induced-fit molecular mimicry underpins TRAV27/TRBV19(+)TCR specificity for the WT and mutant M158peptides, suggesting the possibility of universal CTL immunity in HLA-A*0201(+)individuals. Combined with the high population frequency of HLA-A*0201, these data potentially explain the relative conservation of M158 Moreover, our results suggest that vaccination strategies aimed at generating broad protection should incorporate variant peptides to elicit cross-reactive responses against other specificities, especially those that may be relatively infrequent among IAV-primed memory CTLs.
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Komadina N, Quiñones-Parra SM, Kedzierska K, McCaw JM, Kelso A, Leder K, McVernon J. High conservation level of CD8(+) T cell immunogenic regions within an unusual H1N2 human influenza variant. J Med Virol 2016; 88:1725-32. [PMID: 26950895 DOI: 10.1002/jmv.24516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 12/23/2022]
Abstract
Current seasonal influenza vaccines require regular updates due to antigenic drift causing loss of effectiveness and therefore providing little or no protection against novel influenza A subtypes. Next generation vaccines capable of eliciting CD8(+) T cell (CTL) mediated cross-protective immunity may offer a long-term alternative strategy. However, measuring pre- and existing levels of CTL cross-protection in humans is confounded by differences in infection histories across individuals. During 2000-2003, H1N2 viruses circulated persistently in the human population for the first time and we hypothesized that the viral nucleoprotein (NP) contained novel CTL epitopes that may have contributed to the survival of the viruses. This study describes the immunogenic NP peptides of H1N1, H2N2, and H3N2 influenza viruses isolated from humans over the past century, 1918-2003, by comparing this historical dataset to reference NP peptides from H1N2 that circulated in humans during 2000-2003. Observed peptides sequences ranged from highly conserved (15%) to highly variable (12%), with variation unrelated to reported immunodominance. No unique NP peptides which were exclusive to the H1N2 viruses were noted. However, the virus had inherited the NP from a recently emerged H3N2 variant containing novel peptides, which may have assisted its persistence. Any advantage due to this novelty was subsequently lost with emergence of a newer H3N2 variant in 2003. Our approach has potential to provide insight into the population context in which influenza viruses emerge, and may help to inform immunogenic peptide selection for CTL-inducing influenza vaccines. J. Med. Virol. 88:1725-1732, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Naomi Komadina
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia.,The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Sergio M Quiñones-Parra
- The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia.,The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia.,The University of Melbourne, Melbourne, Victoria, Australia
| | - James M McCaw
- The University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
| | - Anne Kelso
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia.,The Peter Doherty Institute of Infection and Immunity, Melbourne, Australia.,The University of Melbourne, Melbourne, Victoria, Australia
| | - Karin Leder
- Monash University, Melbourne, Victoria, Australia.,Victorian Infectious Diseases Services, Melbourne, Victoria, Australia
| | - Jodie McVernon
- The University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
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25
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Differential Recognition of Influenza A Viruses by M158-66 Epitope-Specific CD8+ T Cells Is Determined by Extraepitopic Amino Acid Residues. J Virol 2015; 90:1009-22. [PMID: 26537686 DOI: 10.1128/jvi.02439-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/29/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Natural influenza A virus infections elicit both virus-specific antibody and CD4(+) and CD8(+) T cell responses. Influenza A virus-specific CD8(+) cytotoxic T lymphocytes (CTLs) contribute to clearance of influenza virus infections. Viral CTL epitopes can display variation, allowing influenza A viruses to evade recognition by epitope-specific CTLs. Due to functional constraints, some epitopes, like the immunodominant HLA-A*0201-restricted matrix protein 1 (M158-66) epitope, are highly conserved between influenza A viruses regardless of their subtype or host species of origin. We hypothesized that human influenza A viruses evade recognition of this epitope by impairing antigen processing and presentation by extraepitopic amino acid substitutions. Activation of specific T cells was used as an indication of antigen presentation. Here, we show that the M158-66 epitope in the M1 protein derived from human influenza A virus was poorly recognized compared to the M1 protein derived from avian influenza A virus. Furthermore, we demonstrate that naturally occurring variations at extraepitopic amino acid residues affect CD8(+) T cell recognition of the M158-66 epitope. These data indicate that human influenza A viruses can impair recognition by M158-66-specific CTLs while retaining the conserved amino acid sequence of the epitope, which may represent a yet-unknown immune evasion strategy for influenza A viruses. This difference in recognition may have implications for the viral replication kinetics in HLA-A*0201 individuals and spread of influenza A viruses in the human population. The findings may aid the rational design of universal influenza vaccines that aim at the induction of cross-reactive virus-specific CTL responses. IMPORTANCE Influenza viruses are an important cause of acute respiratory tract infections. Natural influenza A virus infections elicit both humoral and cellular immunity. CD8(+) cytotoxic T lymphocytes (CTLs) are directed predominantly against conserved internal proteins and confer cross-protection, even against influenza A viruses of various subtypes. In some CTL epitopes, mutations occur that allow influenza A viruses to evade recognition by CTLs. However, the immunodominant HLA-A*0201-restricted M158-66 epitope does not tolerate mutations without loss of viral fitness. Here, we describe naturally occurring variations in amino acid residues outside the M158-66 epitope that influence the recognition of the epitope. These results provide novel insights into the epidemiology of influenza A viruses and their pathogenicity and may aid rational design of vaccines that aim at the induction of CTL responses.
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26
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van de Sandt CE, Bodewes R, Rimmelzwaan GF, de Vries RD. Influenza B viruses: not to be discounted. Future Microbiol 2015; 10:1447-65. [PMID: 26357957 DOI: 10.2217/fmb.15.65] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In contrast to influenza A viruses, which have been investigated extensively, influenza B viruses have attracted relatively little attention. However, influenza B viruses are an important cause of morbidity and mortality in the human population and full understanding of their biological and epidemiological properties is imperative to better control this important pathogen. However, some of its characteristics are still elusive and warrant investigation. Here, we review evolution, epidemiology, pathogenesis and immunity and identify gaps in our knowledge of influenza B viruses. The divergence of two antigenically distinct influenza B viruses is highlighted. The co-circulation of viruses of these two lineages necessitated the development of quadrivalent influenza vaccines, which is discussed in addition to possibilities to develop universal vaccination strategies.
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Affiliation(s)
- Carolien E van de Sandt
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Guus F Rimmelzwaan
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,ViroClinics Biosciences BV, Rotterdam Science Tower, Marconistraat 16, 3029 AK Rotterdam, The Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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27
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Altenburg AF, Rimmelzwaan GF, de Vries RD. Virus-specific T cells as correlate of (cross-)protective immunity against influenza. Vaccine 2015; 33:500-6. [DOI: 10.1016/j.vaccine.2014.11.054] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/30/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022]
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28
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La Gruta NL, Turner SJ. T cell mediated immunity to influenza: mechanisms of viral control. Trends Immunol 2014; 35:396-402. [PMID: 25043801 DOI: 10.1016/j.it.2014.06.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 06/20/2014] [Accepted: 06/20/2014] [Indexed: 12/31/2022]
Abstract
Infection with influenza A virus (IAV) is a major cause of worldwide morbidity and mortality. Recent findings indicate that T cell immunity is key to limiting severity of disease arising from IAV infection, particularly in instances where antibody immunity is ineffective. As such, there is a need to understand better the mechanisms that mediate effective IAV-specific cellular immunity, especially given that T cell immunity must form an integral part of any vaccine designed to elicit crossreactive immunity against existing and new strains of influenza virus. Here, we review the current understanding of cellular immunity to IAV, highlighting recent findings that demonstrate important roles for both CD4+ and CD8+ T cell immunity in protection from IAV-mediated disease.
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Affiliation(s)
- Nicole L La Gruta
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Stephen J Turner
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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29
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The domain landscape of virus-host interactomes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:867235. [PMID: 24991570 PMCID: PMC4065681 DOI: 10.1155/2014/867235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
Viral infections result in millions of deaths in the world today. A thorough analysis of virus-host interactomes may reveal insights into viral infection and pathogenic strategies. In this study, we presented a landscape of virus-host interactomes based on protein domain interaction. Compared to the analysis at protein level, this domain-domain interactome provided a unique abstraction of protein-protein interactome. Through comparisons among DNA, RNA, and retrotranscribing viruses, we identified a core of human domains, that viruses used to hijack the cellular machinery and evade the immune system, which might be promising antiviral drug targets. We showed that viruses preferentially interacted with host hub and bottleneck domains, and the degree and betweenness centrality among three categories of viruses are significantly different. Further analysis at functional level highlighted that different viruses perturbed the host cellular molecular network by common and unique strategies. Most importantly, we creatively proposed a viral disease network among viral domains, human domains and the corresponding diseases, which uncovered several unknown virus-disease relationships that needed further verification. Overall, it is expected that the findings will help to deeply understand the viral infection and contribute to the development of antiviral therapy.
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30
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Epistatically interacting substitutions are enriched during adaptive protein evolution. PLoS Genet 2014; 10:e1004328. [PMID: 24811236 PMCID: PMC4014419 DOI: 10.1371/journal.pgen.1004328] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/10/2014] [Indexed: 01/12/2023] Open
Abstract
Most experimental studies of epistasis in evolution have focused on adaptive changes—but adaptation accounts for only a portion of total evolutionary change. Are the patterns of epistasis during adaptation representative of evolution more broadly? We address this question by examining a pair of protein homologs, of which only one is subject to a well-defined pressure for adaptive change. Specifically, we compare the nucleoproteins from human and swine influenza. Human influenza is under continual selection to evade recognition by acquired immune memory, while swine influenza experiences less such selection due to the fact that pigs are less likely to be infected with influenza repeatedly in a lifetime. Mutations in some types of immune epitopes are therefore much more strongly adaptive to human than swine influenza—here we focus on epitopes targeted by human cytotoxic T lymphocytes. The nucleoproteins of human and swine influenza possess nearly identical numbers of such epitopes. However, mutations in these epitopes are fixed significantly more frequently in human than in swine influenza, presumably because these epitope mutations are adaptive only to human influenza. Experimentally, we find that epistatically constrained mutations are fixed only in the adaptively evolving human influenza lineage, where they occur at sites that are enriched in epitopes. Overall, our results demonstrate that epistatically interacting substitutions are enriched during adaptation, suggesting that the prevalence of epistasis is dependent on the underlying evolutionary forces at play. Mutations can fix during evolution for two reasons: they can be beneficial and fix for adaptive reasons, or they can be neutral or deleterious and fix solely by chance. Most studies focus on adaptation, where the evolving population is increasing in fitness due to a new selection pressure. Such studies have found an important evolutionary role for epistasis, the phenomenon where the effect of one mutation depends on another mutation. But adaptation only accounts for a fraction of overall evolutionary change. Here we investigate whether epistasis is as common during non-adaptive as adaptive evolution. We do this by comparing the same protein from human and swine influenza. Human influenza is constantly adapting to escape from the immunity that people acquire from previous influenza infections. But swine influenza is under less pressure to escape from acquired immunity since pigs have shorter lifetimes and are less likely to be infected with influenza multiple times. We find that epistasis is less common during the evolution of the swine influenza protein than its human influenza counterpart. Overall, our results suggest that mutations that interact via epistasis are more likely to fix during adaptive evolution.
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31
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Akram A, Inman RD. Co-expression of HLA-B7 and HLA-B27 alleles is associated with B7-restricted immunodominant responses following influenza infection. Eur J Immunol 2013; 43:3254-67. [DOI: 10.1002/eji.201343597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 07/11/2013] [Accepted: 09/23/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Ali Akram
- Division of Genetics and Development; Toronto Western Research Institute; Toronto Ontario Canada
- Department of Immunology; Faculty of Medicine; Institute of Medical Sciences; University of Toronto; Toronto Ontario Canada
| | - Robert D. Inman
- Department of Medicine; Faculty of Medicine; University of Toronto; Toronto Ontario Canada
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32
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Targeted delivery of an antigenic peptide to the endoplasmic reticulum: application for development of a peptide therapy for ankylosing spondylitis. PLoS One 2013; 8:e77451. [PMID: 24155957 PMCID: PMC3796468 DOI: 10.1371/journal.pone.0077451] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/04/2013] [Indexed: 12/03/2022] Open
Abstract
The development of suitable methods to deliver peptides specifically to the endoplasmic reticulum (ER) can provide some potential therapeutic applications of such peptides. Ankylosing spondylitis (AS) is strongly associated with the expression of human leukocytic antigen-B27 (HLA-B27). HLA-B27 heavy chain (HC) has a propensity to fold slowly resulting in the accumulation of misfolded HLA-B27 HC in the ER, triggering the unfolded protein response, and forming a homodimer, (B27-HC)2. Natural killer cells and T-helper 17 cells are then activated, contributing to the major pathogenic potentials of AS. The HLA-B27 HC is thus an important target, and delivery of an HLA-B27-binding peptide to the ER capable of promoting HLA-B27 HC folding is a potential mechanism for AS therapy. Here, we demonstrate that a His6-ubiquitin-tagged Tat-derived peptide (THU) can deliver an HLA-B27-binding peptide to the ER promoting HLA-B27 HC folding. The THU-HLA-B27-binding peptide fusion protein crossed the cell membrane to the cytosol through the Tat-derived peptide. The HLA-B27-binding peptide was specifically cleaved from THU by cytosolic ubiquitin C-terminal hydrolases and subsequently transported into the ER by the transporter associated with antigen processing. This approach has potential application in the development of peptide therapy for AS.
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33
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In vitro assessment of the immunological significance of a human monoclonal antibody directed to the influenza a virus nucleoprotein. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1333-7. [PMID: 23761662 DOI: 10.1128/cvi.00339-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Influenza A viruses cause annual epidemics and occasionally pandemics. Antibodies directed to the conserved viral nucleoprotein (NP) may play a role in immunity against various influenza A virus subtypes. Here, we assessed the immunological significance of a human monoclonal antibody directed to NP in vitro. This antibody bound to virus-infected cells but did not display virus-neutralizing activity, complement-dependent cell cytotoxicity, or opsonization of viral antigen for improved antigen presentation to CD8(+) T cells by dendritic cells.
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34
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Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2013; 2:e00631. [PMID: 23682315 PMCID: PMC3654441 DOI: 10.7554/elife.00631] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/09/2013] [Indexed: 11/28/2022] Open
Abstract
John Maynard Smith compared protein evolution to the game where one word is converted into another a single letter at a time, with the constraint that all intermediates are words: WORD→WORE→GORE→GONE→GENE. In this analogy, epistasis constrains evolution, with some mutations tolerated only after the occurrence of others. To test whether epistasis similarly constrains actual protein evolution, we created all intermediates along a 39-mutation evolutionary trajectory of influenza nucleoprotein, and also introduced each mutation individually into the parent. Several mutations were deleterious to the parent despite becoming fixed during evolution without negative impact. These mutations were destabilizing, and were preceded or accompanied by stabilizing mutations that alleviated their adverse effects. The constrained mutations occurred at sites enriched in T-cell epitopes, suggesting they promote viral immune escape. Our results paint a coherent portrait of epistasis during nucleoprotein evolution, with stabilizing mutations permitting otherwise inaccessible destabilizing mutations which are sometimes of adaptive value. DOI:http://dx.doi.org/10.7554/eLife.00631.001 During evolution, the effect of one mutation on a protein can depend on whether another mutation is also present. This phenomenon is similar to the game in which one word is converted to another word, one letter at a time, subject to the rule that all the intermediate steps are also valid words: for example, the word WORD can be converted to the word GENE as follows: WORD→WORE→GORE→GONE→GENE. In this example, the D must be changed to an E before the W is changed to a G, because GORD is not a valid word. Similarly, during the evolution of a virus, a mutation that helps the virus evade the human immune system might only be tolerated if the virus has acquired another mutation beforehand. This type of mutational interaction would constrain the evolution of the virus, since its capacity to take advantage of the second mutation depends on the first mutation having already occurred. Gong et al. examined whether such interactions have indeed constrained evolution of the influenza virus. Between 1968 and 2007, the nucleoprotein—which acts as a scaffold for the replication of genetic material—in the human H3N2 influenza virus underwent a series of 39 mutations. To test whether all of these mutations could have been tolerated by the 1968 virus, Gong et al. introduced each one individually into the 1968 nucleoprotein. They found that several mutations greatly reduced the fitness of the 1968 virus when introduced on their own, which strongly suggests that these ‘constrained mutations’ became part of the virus’s genetic makeup as a result of interactions with ‘enabling’ mutations. The constrained mutations decreased the stability of the nucleoprotein at high temperatures, while the enabling mutations counteracted this effect. It may, therefore, be possible to identify enabling mutations based on their effects on thermal stability. Intriguingly, the constrained mutations helped the virus overcome one form of human immunity to influenza, suggesting that interactions between mutations might limit the rate at which viruses evolve to evade the immune system. Overall, these results show that interactions among mutations constrain the evolution of the influenza nucleoprotein in a fashion that can be largely understood in terms of protein stability. If the same is true for other proteins and viruses, this work could lead to a deeper understanding of the constraints that govern evolution at the molecular level. DOI:http://dx.doi.org/10.7554/eLife.00631.002
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Affiliation(s)
- Lizhi Ian Gong
- Division of Basic Sciences , Fred Hutchinson Cancer Research Center , Seattle , United States
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35
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The design and proof of concept for a CD8(+) T cell-based vaccine inducing cross-subtype protection against influenza A virus. Immunol Cell Biol 2012; 91:96-104. [PMID: 23146941 DOI: 10.1038/icb.2012.54] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, we examined the reactivity of human peripheral blood mononuclear cells to a panel of influenza A virus (IAV) CD8(+) T-cell epitopes that are recognised by the major human leukocyte antigen (HLA) groups represented in the human population. We examined the level of recognition in a sample of the human population and the potential coverage that could be achieved if these were incorporated into a T-cell epitope-based vaccine. We then designed a candidate influenza vaccine that incorporated three of the examined HLA-A2-restricted influenza epitopes into Pam2Cys-based lipopeptides. These lipopeptides do not require the addition of an adjuvant and can be delivered directly to the respiratory mucosa enabling the generation of local memory cell populations that are crucial for clearance of influenza. Intranasal administration of a mixture of three lipopeptides to HLA-A2 transgenic HHD mice elicited multiple CD8(+) T-cell specificities in the spleen and lung that closely mimicked the response generated following natural infection with influenza. These CD8(+) T cells were associated with viral reduction following H3N1 influenza virus challenge for as long as 3 months after lipopeptide administration. In addition, lipopeptides containing IAV-targeting epitopes conferred substantial benefit against death following infection with a virulent H1N1 strain. Because CD8(+) T cell epitopes are often derived from highly conserved regions of influenza viruses, such vaccines need not be reformulated annually and unlike current antibody-inducing vaccines could provide cross-protective immunity against newly emerging pandemic viruses.
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La Gruta N, Kelso A, Brown LE, Chen W, Jackson DC, Turner SJ. Role of CD8(+) T-cell immunity in influenza infection: potential use in future vaccine development. Expert Rev Respir Med 2012; 3:523-37. [PMID: 20477341 DOI: 10.1586/ers.09.44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Continued circulation of the highly pathogenic avian H5N1 influenza A virus has many people worried that an influenza pandemic is imminent. Compounding this is the realization that H5N1 vaccines based on current influenza vaccine technology (designed to generate protective antibody responses) may be suboptimal at providing protection. As a consequence, there is recent interest in vaccine strategies that elicit cellular immunity, particularly the cytotoxic T lymphocyte response, in an effort to provide protection against a potential pandemic. A major issue is the lack of information about the precise role that these 'hitmen' of the immune system have in protecting against both pandemic and seasonal influenza. We need to know more about how the induction and maintenance of cytotoxic T lymphocytes after influenza infection can impact protection from further infection. The challenge is then to use this information in the design of vaccines that will protect against pandemic influenza and will help optimize CD8(+) killer T-cell responses in other infections.
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Affiliation(s)
- Nicole La Gruta
- Department of Microbiology and Immunology, The University of Melbourne, Royal Parade, Parkville, Victoria 3010, Australia
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van de Sandt CE, Kreijtz JHCM, Rimmelzwaan GF. Evasion of influenza A viruses from innate and adaptive immune responses. Viruses 2012; 4:1438-76. [PMID: 23170167 PMCID: PMC3499814 DOI: 10.3390/v4091438] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/10/2012] [Accepted: 08/22/2012] [Indexed: 12/16/2022] Open
Abstract
The influenza A virus is one of the leading causes of respiratory tract infections in humans. Upon infection with an influenza A virus, both innate and adaptive immune responses are induced. Here we discuss various strategies used by influenza A viruses to evade innate immune responses and recognition by components of the humoral and cellular immune response, which consequently may result in reduced clearing of the virus and virus-infected cells. Finally, we discuss how the current knowledge about immune evasion can be used to improve influenza A vaccination strategies.
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Affiliation(s)
- Carolien E van de Sandt
- Department of Virology, ErasmusMC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.
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Qiu X, Hong C, Li Y, Bao W, Gao XM. Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus. Microbiol Immunol 2012; 56:554-61. [PMID: 22530918 PMCID: PMC7168421 DOI: 10.1111/j.1348-0421.2012.00467.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 12/02/2022]
Abstract
Fragment 450-650 of the spike (S) protein (S450-650) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains epitopes capable of being recognized by convalescent sera of SARS patients. Vaccination of mice with recombinant S450-650 (rS450-650) can induce Abs against SARS-CoV, although the titer is relatively low. In the present study, a fusion protein linking a fragment (residues 39-272) of murine calreticulin (CRT) to S450-650 in a prokaryotic expression system was created. Compared with target antigen alone, the recombinant fusion product (rS450-650-CRT) has much improved hydrophilicity and immunogenicity. The S450-650-specific IgG Abs of BALB/c mice subcutaneously immunized with rS450-650-CRT were in substantially higher titer (approximately fivefold more). Furthermore, the fusion protein, but not rS450-650 alone, was able to elicit S450-650-specific IgG responses in T cell deficient nude mice. Given that rCRT/39-272 can drive the maturation of bone-marrow-derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39-272 of CRT is an effective molecular adjuvant capable of enhancing target Ag-specific humoral responses in both a T cell-dependent and independent manner. Fusion protein rS450-650-CRT is a potential candidate vaccine against SARS-CoV infection.
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Affiliation(s)
- Xiang Qiu
- Department of Immunology, Peking University Health Science Center, Beijing, China
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39
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Immunodominance: a pivotal principle in host response to viral infections. Clin Immunol 2012; 143:99-115. [PMID: 22391152 DOI: 10.1016/j.clim.2012.01.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 11/24/2022]
Abstract
We encounter pathogens on a daily basis and our immune system has evolved to mount an immune response following an infection. An interesting phenomenon that has evolved in response to clearing bacterial and viral infections is called immunodominance. Immunodominance refers to the phenomenon that, despite co-expression of multiple major histocompatibility complex class I alleles by host cells and the potential generation of hundreds of distinct antigenic peptides for recognition following an infection, a large portion of the anti-viral cytotoxic T lymphocyte population targets only some peptide/MHC class I complexes. Here we review the main factors contributing to immunodominance in relation to influenza A and HIV infection. Of special interest are the factors contributing to immunodominance in humans and rodents following influenza A infection. By critically reviewing these findings, we hope to improve understanding of the challenges facing the discovery of new factors enabling better anti-viral vaccine strategies in the future.
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40
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Homan EJ, Bremel RD. Patterns of predicted T-cell epitopes associated with antigenic drift in influenza H3N2 hemagglutinin. PLoS One 2011; 6:e26711. [PMID: 22039539 PMCID: PMC3200361 DOI: 10.1371/journal.pone.0026711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 10/03/2011] [Indexed: 12/19/2022] Open
Abstract
Antigenic drift allowing escape from neutralizing antibodies is an important feature of transmission and survival of influenza viruses in host populations. Antigenic drift has been studied in particular detail for influenza A H3N2 and well defined antigenic clusters of this virus documented. We examine how host immunogenetics contributes to determination of the antibody spectrum, and hence the immune pressure bringing about antigenic drift. Using uTOPE™ bioinformatics analysis of predicted MHC binding, based on amino acid physical property principal components, we examined the binding affinity of all 9-mer and 15-mer peptides within the hemagglutinin 1 (HA1) of 447 H3N2 virus isolates to 35 MHC-I and 14 MHC-II alleles. We provide a comprehensive map of predicted MHC-I and MHC-II binding affinity for a broad array of HLA alleles for the H3N2 influenza HA1 protein. Each HLA allele exhibited a characteristic predicted binding pattern. Cluster analysis for each HLA allele shows that patterns based on predicted MHC binding mirror those described based on antibody binding. A single amino acid mutation or position displacement can result in a marked difference in MHC binding and hence potential T-helper function. We assessed the impact of individual amino acid changes in HA1 sequences between 10 virus isolates from 1968-2002, representative of antigenic clusters, to understand the changes in MHC binding over time. Gain and loss of predicted high affinity MHC-II binding sites with cluster transitions were documented. Predicted high affinity MHC-II binding sites were adjacent to antibody binding sites. We conclude that host MHC diversity may have a major determinant role in the antigenic drift of influenza A H3N2.
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Affiliation(s)
- E Jane Homan
- ioGenetics LLC, Madison, Wisconsin, United States of America.
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41
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Induction of virus-specific cytotoxic T lymphocytes as a basis for the development of broadly protective influenza vaccines. J Biomed Biotechnol 2011; 2011:939860. [PMID: 22007149 PMCID: PMC3189652 DOI: 10.1155/2011/939860] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/01/2011] [Accepted: 08/02/2011] [Indexed: 11/18/2022] Open
Abstract
There is considerable interest in the development of broadly protective influenza vaccines because of the continuous emergence of antigenic drift variants of seasonal influenza viruses and the threat posed by the emergence of antigenically distinct pandemic influenza viruses. It has been recognized more than three decades ago that influenza A virus-specific cytotoxic T lymphocytes recognize epitopes located in the relatively conserved proteins like the nucleoprotein and that they cross-react with various subtypes of influenza A viruses. This implies that these CD8+ T lymphocytes may contribute to protective heterosubtypic immunity induced by antecedent influenza A virus infections. In the present paper, we review the evidence for the role of virus-specific CD8+ T lymphocytes in protective immunity against influenza virus infections and discuss vaccination strategies that aim at the induction of cross-reactive virus-specific T-cell responses.
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Kreijtz JHCM, Fouchier RAM, Rimmelzwaan GF. Immune responses to influenza virus infection. Virus Res 2011; 162:19-30. [PMID: 21963677 DOI: 10.1016/j.virusres.2011.09.022] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/15/2011] [Accepted: 09/15/2011] [Indexed: 10/17/2022]
Abstract
Influenza viruses cause annual outbreaks of respiratory tract infection with attack rates of 5-10%. This means that humans are infected repeatedly with intervals of, on average, 10-20 years. Upon each infection subjects develop innate and adaptive immune responses which aim at clearing the infection. Strain-specific antibody responses are induced, which exert selective pressure on circulating influenza viruses and which drive antigenic drift of seasonal influenza viruses, especially in the hemagglutinin molecule. This antigenic drift necessitates updating of seasonal influenza vaccines regularly in order to match the circulating strains. Upon infection also virus-specific T cell responses are induced, including CD4+ T helper cells and CD8+ cytotoxic T cells. These cells are mainly directed to conserved proteins and therefore display cross-reactivity with a variety of influenza A viruses of different subtypes. T cell mediated immunity therefore may contribute to so-called heterosubtypic immunity and may afford protection against antigenically distinct, potentially pandemic influenza viruses. At present, novel viral targets are identified that may help to develop broad-protective vaccines. Here we review the various arms of the immune response to influenza virus infections and their viral targets and discuss the possibility of developing universal vaccines. The development of such novel vaccines would imply that also new immune correlates of protection need to be established in order to facilitate assessment of vaccine efficacy.
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Affiliation(s)
- J H C M Kreijtz
- Department of Virology, Erasmus MC, Rotterdam, The Netherlands
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43
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Abstract
The swine, influenza, H1N1 outbreak in 2009 highlighted the inadequacy of the currently used antibody-based vaccine strategies as a preventive measure for combating influenza pandemics. The ultimate goal for successful control of newly arising influenza outbreaks is to design a single-shot vaccine that will provide long-lasting immunity against all strains of influenza A virus. A large amount of data from animal studies has indicated that the cross-reactive cytotoxic T (Tc) cell response against conserved influenza virus epitopes may be the key immune response needed for a universal influenza vaccine. However, decades of research have shown that the development of safe T-cell-based vaccines for influenza is not an easy task. Here, I discuss the overlooked but potentially highly advantageous inactivation method, namely, γ-ray irradiation, as a mean to reach the Holy Grail of influenza vaccinology.
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Affiliation(s)
- Yoichi Furuya
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208-3479, USA.
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44
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Tan ACL, La Gruta NL, Zeng W, Jackson DC. Precursor frequency and competition dictate the HLA-A2-restricted CD8+ T cell responses to influenza A infection and vaccination in HLA-A2.1 transgenic mice. THE JOURNAL OF IMMUNOLOGY 2011; 187:1895-902. [PMID: 21765016 DOI: 10.4049/jimmunol.1100664] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The human HLA-A2-restricted CD8(+) T cell response to influenza A virus (IAV) is largely directed against the matrix protein-derived M1(58-66) epitope and represents an archetypal example of CD8(+) T cell immunodominance. In this study, we examined the CD8(+) T cell hierarchy to M1(58-66) and two subdominant IAV-specific epitopes: NS1(122-130) and PA(46-55) in HLA-A2(+) human subjects and HLA-A2.1 transgenic (HHD) mice. Using epitope-based lipopeptides, we show that the CD8(+) T cell hierarchy induced by IAV infection could also be induced by lipopeptide vaccination in a context outside of viral infection when the Ag load is equalized. In the HHD HLA-A2.1 mouse model, we show that the naive T cell precursor frequencies, and competition at the Ag presentation level, can predict the IAV-specific CD8(+) T cell hierarchy. Immunization of mice with subdominant epitopes alone was unable to overcome the dominance of the M1(58-66)-specific response in the face of IAV challenge; however, a multiepitope vaccination strategy was most effective at generating a broad and multispecific response to infection.
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Affiliation(s)
- Amabel C L Tan
- Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Victoria, Australia
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45
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Venturi V, Davenport MP, Swan NG, Doherty PC, Kedzierska K. Consequences of suboptimal priming are apparent for low-avidity T-cell responses. Immunol Cell Biol 2011; 90:216-23. [PMID: 21556018 DOI: 10.1038/icb.2011.36] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The emergence of the novel reassortant A(H1N1)-2009 influenza virus highlighted the threat to the global population posed by an influenza pandemic. Pre-existing CD8(+) T-cell immunity targeting conserved epitopes provides immune protection against newly emerging strains of influenza virus, when minimal antibody immunity exists. However, the occurrence of mutations within T-cell antigenic peptides that enable the virus to evade T-cell recognition constitutes a substantial issue for virus control and vaccine design. Recent evidence suggests that it might be feasible to elicit CD8(+) T-cell memory pools to common virus mutants by pre-emptive vaccination. However, there is a need for a greater understanding of CD8(+) T-cell immunity towards commonly emerging mutants. The present analysis focuses on novel and immunodominant, although of low pMHC-I avidity, CD8(+) T-cell responses directed at the mutant influenza D(b)NP(366) epitope, D(b)NPM6A, following different routes of infection. We used a C57BL/6J model of influenza to dissect the effectiveness of the natural intranasal (i.n.) versus intraperitoneal (i.p.) priming for generating functional CD8(+) T cells towards the D(b)NPM6A epitope. In contrast to comparable CD8(+) T-cell responses directed at the wild-type epitopes, D(b)NP(366) and D(b)PA(224), we found that the priming route greatly affected the numbers, cytokine profiles and TCR repertoire of the responding CD8(+) T cells directed at the D(b)NPM6A viral mutant. As the magnitude, polyfunctionality, and T-cell repertoire diversity are potential determinants of the protective efficacy of CD8(+) T-cell responses, our data have implications for the development of vaccines to combat virus mutants.
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Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
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46
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Redundancy of the influenza A virus-specific cytotoxic T lymphocyte response in HLA-B*2705 transgenic mice limits the impact of a mutation in the immunodominant NP383–391 epitope on influenza pathogenesis. Virus Res 2011; 155:123-30. [DOI: 10.1016/j.virusres.2010.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 09/14/2010] [Accepted: 09/14/2010] [Indexed: 12/24/2022]
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Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS One 2010; 5:e8754. [PMID: 20090904 PMCID: PMC2807450 DOI: 10.1371/journal.pone.0008754] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 12/23/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The immune-related evolution of influenza viruses is exceedingly complex and current vaccines against influenza must be reformulated for each influenza season because of the high degree of antigenic drift among circulating influenza strains. Delay in vaccine production is a serious problem in responding to a pandemic situation, such as that of the current H1N1 strain. Immune escape is generally attributed to reduced antibody recognition of the viral hemagglutinin and neuraminidase proteins whose rate of mutation is much greater than that of the internal non-structural proteins. As a possible alternative, vaccines directed at T cell epitope domains of internal influenza proteins, that are less susceptible to antigenic variation, have been investigated. METHODOLOGY/PRINCIPAL FINDINGS HLA transgenic mouse strains expressing HLA class I A*0201, A*2402, and B*0702, and class II DRB1*1501, DRB1*0301 and DRB1*0401 were immunized with 196 influenza H1N1 peptides that contained residues of highly conserved proteome sequences of the human H1N1, H3N2, H1N2, H5N1, and avian influenza A strains. Fifty-four (54) peptides that elicited 63 HLA-restricted peptide-specific T cell epitope responses were identified by IFN-gamma ELISpot assay. The 54 peptides were compared to the 2007-2009 human H1N1 sequences for selection of sequences in the design of a new candidate H1N1 vaccine, specifically targeted to highly-conserved HLA-restricted T cell epitopes. CONCLUSIONS/SIGNIFICANCE Seventeen (17) T cell epitopes in PB1, PB2, and M1 were selected as vaccine targets based on sequence conservation over the past 30 years, high functional avidity, non-identity to human peptides, clustered localization, and promiscuity to multiple HLA alleles. These candidate vaccine antigen sequences may be applicable to any avian or human influenza A virus.
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48
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Targets for the induction of protective immunity against influenza a viruses. Viruses 2010; 2:166-188. [PMID: 21994606 PMCID: PMC3185556 DOI: 10.3390/v2010166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 01/04/2010] [Accepted: 01/13/2010] [Indexed: 01/09/2023] Open
Abstract
The current pandemic caused by the new influenza A(H1N1) virus of swine origin and the current pandemic threat caused by the highly pathogenic avian influenza A viruses of the H5N1 subtype have renewed the interest in the development of vaccines that can induce broad protective immunity. Preferably, vaccines not only provide protection against the homologous strains, but also against heterologous strains, even of another subtype. Here we describe viral targets and the arms of the immune response involved in protection against influenza virus infections such as antibodies directed against the hemagglutinin, neuraminidase and the M2 protein and cellular immune responses directed against the internal viral proteins.
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49
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Liu X, Zhao YP. Switch region for pathogenic structural change in conformational disease and its prediction. PLoS One 2010; 5:e8441. [PMID: 20111584 PMCID: PMC2801591 DOI: 10.1371/journal.pone.0008441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 11/27/2009] [Indexed: 11/19/2022] Open
Abstract
Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.
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Affiliation(s)
- Xin Liu
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Ya-Pu Zhao
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
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50
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Rimmelzwaan GF, Kreijtz JHCM, Bodewes R, Fouchier RAM, Osterhaus ADME. Influenza virus CTL epitopes, remarkably conserved and remarkably variable. Vaccine 2009; 27:6363-5. [PMID: 19840674 DOI: 10.1016/j.vaccine.2009.01.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 01/06/2009] [Accepted: 01/08/2009] [Indexed: 01/05/2023]
Abstract
Virus-specific cytotoxic T lymphocytes (CTL) contribute to the control of virus infections including those caused by influenza viruses. Especially under circumstances when antibodies induced by previous infection or vaccination fail to recognize and neutralize the virus adequately, CTL are important and contribute to protective immunity. During epidemic outbreaks caused by antigenic drift variants and during pandemic outbreaks of influenza, humoral immunity against influenza viruses is inadequate. Under these circumstances, pre-existing CTL directed to the relatively conserved internal proteins of the virus may provide cross-protective immunity. Indeed, most of the known human influenza virus CTL epitopes are conserved. However, during the evolution of influenza A/H3N2 viruses, the most important cause of seasonal influenza outbreaks, variation in CTL epitopes has been observed. The observed amino acid substitutions affected recognition by virus-specific CTL and the human virus-specific CTL response in vitro. Examples of variable epitopes and their HLA restrictions are: NP(383-391)/HLA-B*2705, NP(380-388)/HLA-B*0801, NP(418-426)/HLA-B*3501, NP(251-259)/HLA-B*4002, NP(103-111)/HLA-B*1503. In some cases amino acid substitutions occurred at anchor residues and in other cases at T cell receptor contact residues. It is of special interest that the R384G substitution in the NP(383-391) epitope was detrimental to virus fitness and was only tolerated in the presence of multiple functionally compensating co-mutations. In contrast, other epitopes, like the HLA-A*0201 restricted epitope from the matrix protein, M1(58-66), are highly conserved despite their immunodominant nature and the high prevalence of HLA-A*0201 in the population. A mutational analysis of this epitope indicated that it is under functional constraints. Also in influenza A viruses of other subtypes, including H5N1, the M1(58-66) is highly conserved.
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Affiliation(s)
- Guus F Rimmelzwaan
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands.
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