1
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Reuschl AK, Thorne LG, Whelan MVX, Ragazzini R, Furnon W, Cowton VM, De Lorenzo G, Mesner D, Turner JLE, Dowgier G, Bogoda N, Bonfanti P, Palmarini M, Patel AH, Jolly C, Towers GJ. Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants. Nat Microbiol 2024; 9:451-463. [PMID: 38228858 PMCID: PMC10847042 DOI: 10.1038/s41564-023-01588-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human adaptation resulted in distinct lineages with enhanced transmissibility called variants of concern (VOCs). Omicron is the first VOC to evolve distinct globally dominant subvariants. Here we compared their replication in human cell lines and primary airway cultures and measured host responses to infection. We discovered that subvariants BA.4 and BA.5 have improved their suppression of innate immunity when compared with earlier subvariants BA.1 and BA.2. Similarly, more recent subvariants (BA.2.75 and XBB lineages) also triggered reduced innate immune activation. This correlated with increased expression of viral innate antagonists Orf6 and nucleocapsid, reminiscent of VOCs Alpha to Delta. Increased Orf6 levels suppressed host innate responses to infection by decreasing IRF3 and STAT1 signalling measured by transcription factor phosphorylation and nuclear translocation. Our data suggest that convergent evolution of enhanced innate immune antagonist expression is a common pathway of human adaptation and link Omicron subvariant dominance to improved innate immune evasion.
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Affiliation(s)
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
- Department of Infectious Diseases, St Mary's Medical School, Imperial College London, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L E Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Giulia Dowgier
- Division of Infection and Immunity, University College London, London, UK
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Nathasha Bogoda
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | | | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
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2
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Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
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Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
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3
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Cowton VM, Dunlop JI, Cole SJ, Swann RE, Patel AH. The Neutralizing Antibody Responses of Individuals That Spontaneously Resolve Hepatitis C Virus Infection. Viruses 2022; 14:v14071391. [PMID: 35891372 PMCID: PMC9318067 DOI: 10.3390/v14071391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major global health problem. In the majority of cases the virus is not cleared by the host immune response and progresses to chronic infection. Studies of the neutralizing antibody responses in individuals that naturally clear infection are limited. Understanding what constitutes a successful antibody response versus one that has 'failed' and resulted in chronic infection is important to understand what type of antibody response would need to be elicited by a protective vaccine. Samples from spontaneous clearers are difficult to obtain therefore studies are often limited. In our study through HCV Research UK, we had access to a cohort of over 200 samples. We identified the samples that contained HCV neutralizing antibodies using ELISA and HCV pseudoparticle (HCVpp) assays. We then utilised mutagenesis and cross-competition analysis to determine the profile of the neutralizing antibody responses. In addition, we analysed a cohort of samples from chronic infection using the same techniques to enable direct comparison of the antibody profiles observed in both cohorts. We conclude that similar profiles are present in both cohorts indicating that it is not the neutralizing antibody response per se that determines the outcome of infection. These data will provide useful information for future HCV vaccine design.
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Affiliation(s)
- Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (J.I.D.); (S.J.C.); (R.E.S.); (A.H.P.)
- Correspondence: ; Tel.: +44-(0)-141-330-2988
| | - James I. Dunlop
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (J.I.D.); (S.J.C.); (R.E.S.); (A.H.P.)
| | - Sarah J. Cole
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (J.I.D.); (S.J.C.); (R.E.S.); (A.H.P.)
| | - Rachael E. Swann
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (J.I.D.); (S.J.C.); (R.E.S.); (A.H.P.)
- Department of Gastroenterology, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (J.I.D.); (S.J.C.); (R.E.S.); (A.H.P.)
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4
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Zhou J, Peacock TP, Brown JC, Goldhill DH, Elrefaey AME, Penrice-Randal R, Cowton VM, De Lorenzo G, Furnon W, Harvey WT, Kugathasan R, Frise R, Baillon L, Lassaunière R, Thakur N, Gallo G, Goldswain H, Donovan-Banfield I, Dong X, Randle NP, Sweeney F, Glynn MC, Quantrill JL, McKay PF, Patel AH, Palmarini M, Hiscox JA, Bailey D, Barclay WS. Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cell Rep 2022; 38:110344. [PMID: 35093235 PMCID: PMC8768428 DOI: 10.1016/j.celrep.2022.110344] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs, and farmed mink. Since the start of the 2019 pandemic, several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all three mink adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ria Lassaunière
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nazia Thakur
- The Pirbright Institute, Woking, Surrey, UK; The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Fiachra Sweeney
- Department of Infectious Disease, Imperial College London, London, UK
| | - Martha C Glynn
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Paul F McKay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A(∗)STAR, Singapore, Singapore
| | | | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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5
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Salas JH, Urbanowicz RA, Guest JD, Frumento N, Figueroa A, Clark KE, Keck Z, Cowton VM, Cole SJ, Patel AH, Fuerst TR, Drummer HE, Major M, Tarr AW, Ball JK, Law M, Pierce BG, Foung SKH, Bailey JR. An Antigenically Diverse, Representative Panel of Envelope Glycoproteins for Hepatitis C Virus Vaccine Development. Gastroenterology 2022; 162:562-574. [PMID: 34655573 PMCID: PMC8792218 DOI: 10.1053/j.gastro.2021.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Development of a prophylactic hepatitis C virus (HCV) vaccine will require accurate and reproducible measurement of neutralizing breadth of vaccine-induced antibodies. Currently available HCV panels may not adequately represent the genetic and antigenic diversity of circulating HCV strains, and the lack of standardization of these panels makes it difficult to compare neutralization results obtained in different studies. Here, we describe the selection and validation of a genetically and antigenically diverse reference panel of 15 HCV pseudoparticles (HCVpps) for neutralization assays. METHODS We chose 75 envelope (E1E2) clones to maximize representation of natural polymorphisms observed in circulating HCV isolates, and 65 of these clones generated functional HCVpps. Neutralization sensitivity of these HCVpps varied widely. HCVpps clustered into 15 distinct groups based on patterns of relative sensitivity to 7 broadly neutralizing monoclonal antibodies. We used these data to select a final panel of 15 antigenically representative HCVpps. RESULTS Both the 65 and 15 HCVpp panels span 4 tiers of neutralization sensitivity, and neutralizing breadth measurements for 7 broadly neutralizing monoclonal antibodies were nearly equivalent using either panel. Differences in neutralization sensitivity between HCVpps were independent of genetic distances between E1E2 clones. CONCLUSIONS Neutralizing breadth of HCV antibodies should be defined using viruses spanning multiple tiers of neutralization sensitivity rather than panels selected solely for genetic diversity. We propose that this multitier reference panel could be adopted as a standard for the measurement of neutralizing antibody potency and breadth, facilitating meaningful comparisons of neutralization results from vaccine studies in different laboratories.
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Affiliation(s)
- Jordan H Salas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Richard A Urbanowicz
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham, United Kingdom; Wolfson Centre for Global Virus Research, The University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
| | - Johnathan D Guest
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Nicole Frumento
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexis Figueroa
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kaitlyn E Clark
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhenyong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Vanessa M Cowton
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sarah J Cole
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H Patel
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Heidi E Drummer
- Viral Entry and Vaccines Group, Burnet Institute, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Marian Major
- Division of Viral Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Alexander W Tarr
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham, United Kingdom; Wolfson Centre for Global Virus Research, The University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
| | - Jonathan K Ball
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham, United Kingdom; Wolfson Centre for Global Virus Research, The University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Justin R Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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6
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Meuleman TJ, Cowton VM, Patel AH, Liskamp RMJ. Design and Synthesis of HCV-E2 Glycoprotein Epitope Mimics in Molecular Construction of Potential Synthetic Vaccines. Viruses 2021; 13:v13020326. [PMID: 33672697 PMCID: PMC7924389 DOI: 10.3390/v13020326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022] Open
Abstract
Hepatitis C virus remains a global threat, despite the availability of highly effective direct-acting antiviral (DAA) drugs. With thousands of new infections annually, the need for a prophylactic vaccine is evident. However, traditional vaccine design has been unable to provide effective vaccines so far. Therefore, alternative strategies need to be investigated. In this work, a chemistry-based approach is explored towards fully synthetic peptide-based vaccines using epitope mimicry, by focusing on highly effective and conserved amino acid sequences in HCV, which, upon antibody binding, inhibit its bio-activity. Continuous and discontinuous epitope mimics were both chemically synthesized based on the HCV-E2 glycoprotein while using designed fully synthetic cyclic peptides. These cyclic epitope mimics were assembled on an orthogonally protected scaffold. The scaffolded epitope mimics have been assessed in immunization experiments to investigate the elicitation of anti-HCV-E2 glycoprotein antibodies. The neutralizing potential of the elicited antibodies was investigated, representing a first step in employing chemically synthesized epitope mimics as a novel strategy towards vaccine design.
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Affiliation(s)
- Theodorus J. Meuleman
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK;
- Enzytag, Daelderweg, 9 6361 HK Nuth, The Netherlands
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK;
- Correspondence: (A.H.P.); (R.M.J.L.)
| | - Rob M. J. Liskamp
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK;
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Faculty of Health, Medicine and Life Sciences, Maastricht UMC, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- Chemical Biology and Drug Discovery, Department of Pharmaceutics, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Cristal Therapeutics, Oxfordlaan 55, 6229 EV Maastricht, The Netherlands
- Correspondence: (A.H.P.); (R.M.J.L.)
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7
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Rihn SJ, Merits A, Bakshi S, Turnbull ML, Wickenhagen A, Alexander AJT, Baillie C, Brennan B, Brown F, Brunker K, Bryden SR, Burness KA, Carmichael S, Cole SJ, Cowton VM, Davies P, Davis C, De Lorenzo G, Donald CL, Dorward M, Dunlop JI, Elliott M, Fares M, da Silva Filipe A, Freitas JR, Furnon W, Gestuveo RJ, Geyer A, Giesel D, Goldfarb DM, Goodman N, Gunson R, Hastie CJ, Herder V, Hughes J, Johnson C, Johnson N, Kohl A, Kerr K, Leech H, Lello LS, Li K, Lieber G, Liu X, Lingala R, Loney C, Mair D, McElwee MJ, McFarlane S, Nichols J, Nomikou K, Orr A, Orton RJ, Palmarini M, Parr YA, Pinto RM, Raggett S, Reid E, Robertson DL, Royle J, Cameron-Ruiz N, Shepherd JG, Smollett K, Stewart DG, Stewart M, Sugrue E, Szemiel AM, Taggart A, Thomson EC, Tong L, Torrie LS, Toth R, Varjak M, Wang S, Wilkinson SG, Wyatt PG, Zusinaite E, Alessi DR, Patel AH, Zaid A, Wilson SJ, Mahalingam S. A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biol 2021; 19:e3001091. [PMID: 33630831 PMCID: PMC7906417 DOI: 10.1371/journal.pbio.3001091] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022] Open
Abstract
The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.
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Affiliation(s)
- Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Matthew L. Turnbull
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Carla Baillie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Steven R. Bryden
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kerry A. Burness
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Sarah J. Cole
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Claire L. Donald
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Mark Dorward
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - James I. Dunlop
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Matthew Elliott
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mazigh Fares
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Joseph R. Freitas
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Rommel J. Gestuveo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Miagao, Iloilo, Philippines
| | - Anna Geyer
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel Giesel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel M. Goldfarb
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Nicola Goodman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, United Kingdom
| | - C. James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Hannah Leech
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | | | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Gauthier Lieber
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Xiang Liu
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Rajendra Lingala
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad Telangana, India
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Marion J. McElwee
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Anne Orr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Yasmin A. Parr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Samantha Raggett
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Elaine Reid
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Jamie Royle
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Natalia Cameron-Ruiz
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - James G. Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Meredith Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Elena Sugrue
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Agnieszka M. Szemiel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Leah S. Torrie
- Drug Discovery Unit (DDU), Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Stuart G. Wilkinson
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul G. Wyatt
- Drug Discovery Unit (DDU), Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ali Zaid
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- School of Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
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8
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Cowton VM, Owsianka AM, Fadda V, Ortega-Prieto AM, Cole SJ, Potter JA, Skelton JK, Jeffrey N, Di Lorenzo C, Dorner M, Taylor GL, Patel AH. Development of a structural epitope mimic: an idiotypic approach to HCV vaccine design. NPJ Vaccines 2021; 6:7. [PMID: 33420102 PMCID: PMC7794244 DOI: 10.1038/s41541-020-00269-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
HCV vaccine development is stymied by the high genetic diversity of the virus and the variability of the envelope glycoproteins. One strategy to overcome this is to identify conserved, functionally important regions—such as the epitopes of broadly neutralizing antibodies (bNAbs)—and use these as a basis for structure-based vaccine design. Here, we report an anti-idiotype approach that has generated an antibody that mimics a highly conserved neutralizing epitope on HCV E2. Crucially, a mutagenesis screen was used to identify the antibody, designated B2.1 A, whose binding characteristics to the bNAb AP33 closely resemble those of the original antigen. Protein crystallography confirmed that B2.1 A is a structural mimic of the AP33 epitope. When used as an immunogen B2.1 A induced antibodies that recognized the same epitope and E2 residues as AP33 and most importantly protected against HCV challenge in a mouse model.
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Affiliation(s)
- Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Ania M Owsianka
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Valeria Fadda
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | | | - Sarah J Cole
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Jane A Potter
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | - Jessica K Skelton
- Section of Virology, Department of Medicine, Imperial College London, London, UK
| | - Nathan Jeffrey
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Caterina Di Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK
| | - Marcus Dorner
- Section of Virology, Department of Medicine, Imperial College London, London, UK
| | - Garry L Taylor
- Biomedical Sciences Research Complex, University of St. Andrews, Fife, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, UK.
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9
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Meuleman TJ, Cowton VM, Patel AH, Liskamp RM. Improving the aqueous solubility of HCV-E2 glycoprotein epitope mimics by cyclization using POLAR hinges. J Pept Sci 2020; 26:e3222. [PMID: 31984607 PMCID: PMC7050536 DOI: 10.1002/psc.3222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022]
Abstract
In this research we describe the improvement of the water-solubility of cyclic epitope mimics based on the HCV E2 glycoprotein by incorporation of suitable polar hinges. The poor solubility of epitope mimics based on peptide sequences in the envelope (E2) protein hampered their synthesis and purification and made it very difficult to prepare the molecular constructs for evaluation of their bioactivity. Since changes in the amino acid composition are hardly possible in these epitope mimics in order to increase water-solubility, a polar cyclization hinge may offer a remedy leading to a significant increase of polarity and therefore water solubility. These polar hinges were applied in the synthesis of better water-soluble HCV-E2 epitopes. An azide functionality in the polar hinges allowed attachment of a tetraethylene glycol linker by Cu-catalyzed azide-alkyne cyclo-addition (CuAAC) for a convenient conjugation to ELISA plates in order to evaluate the bio-activity of the epitope mimics. The immunoassays showed that the use of more polar cyclization hinges still supported anti-HCV antibody recognition and did not negatively influence their binding. This significantly increased solubility induced by polar hinges should therefore allow for the molecular construction and ultimate evaluation of synthetic vaccine molecules.
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Affiliation(s)
- Theodorus J. Meuleman
- School of Chemistry, University of GlasgowJoseph Black Building, University AvenueGlasgowG12 8QQUK
| | - Vanessa M. Cowton
- MRC‐University of Glasgow Centre for Virus ResearchGarscube Campus, Sir Michael Stoker Building, 464 Bearsden RoadGlasgowG61 1QHUK
| | - Arvind H. Patel
- MRC‐University of Glasgow Centre for Virus ResearchGarscube Campus, Sir Michael Stoker Building, 464 Bearsden RoadGlasgowG61 1QHUK
| | - Rob M.J. Liskamp
- School of Chemistry, University of GlasgowJoseph Black Building, University AvenueGlasgowG12 8QQUK
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10
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Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife 2019; 8:42463. [PMID: 31478835 PMCID: PMC6721795 DOI: 10.7554/elife.42463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly variable pathogen that frequently establishes chronic infection. This genetic variability is affected by the adaptive immune response but the contribution of other host factors is unclear. Here, we examined the role played by interferon lambda-4 (IFN-λ4) on HCV diversity; IFN-λ4 plays a crucial role in spontaneous clearance or establishment of chronicity following acute infection. We performed viral genome-wide association studies using human and viral data from 485 patients of white ancestry infected with HCV genotype 3a. We demonstrate that combinations of host genetic variants, which determine IFN-λ4 protein production and activity, influence amino acid variation across the viral polyprotein - not restricted to specific viral proteins or HLA restricted epitopes - and modulate viral load. We also observed an association with viral di-nucleotide proportions. These results support a direct role for IFN-λ4 in exerting selective pressure across the viral genome, possibly by a novel mechanism.
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Affiliation(s)
- M Azim Ansari
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Camilla Lc Ip
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Siu Hin Lau
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Connor Bamford
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - David Bonsall
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Vattipally Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | | | - Emma Hudson
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Graham R Foster
- Blizard Institute, Queen Mary University, London, United Kingdom
| | - William L Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Ca Spencer
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vincent Pedergnana
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.,Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM), Montpellier, France
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11
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Cowton VM, Singer JB, Gifford RJ, Patel AH. Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data. Front Immunol 2018; 9:1470. [PMID: 30013555 PMCID: PMC6036255 DOI: 10.3389/fimmu.2018.01470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is a global health issue. Although direct-acting antivirals are available to target HCV, there is currently no vaccine. The diversity of the virus is a major obstacle to HCV vaccine development. One approach toward a vaccine is to utilize a strategy to elicit broadly neutralizing antibodies (bNAbs) that target highly-conserved epitopes. The conserved epitopes of bNAbs have been mapped almost exclusively to the E2 glycoprotein. In this study, we have used HCV-GLUE, a bioinformatics resource for HCV sequence data, to investigate the major epitopes targeted by well-characterized bNAbs. Here, we analyze the level of conservation of each epitope by genotype and subtype and consider the most promising bNAbs identified to date for further study as potential vaccine leads. For the most conserved epitopes, we also identify the most prevalent sequence variants in the circulating HCV population. We examine the distribution of E2 sequence data from across the globe and highlight regions with no coverage. Genotype 1 is the most prevalent genotype worldwide, but in many regions, it is not the dominant genotype. We find that the sequence conservation data is very encouraging; several bNAbs have a high level of conservation across all genotypes suggesting that it may be unnecessary to tailor vaccines according to the geographical distribution of genotypes.
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Affiliation(s)
| | | | | | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow, Scotland, United Kingdom
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12
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Luke GA, de Felipe P, Cowton VM, Hughes LE, Halpin C, Ryan MD. Self-Processing Polyproteins: A Strategy for Co-expression of Multiple Proteins in Plants. Biotechnol Genet Eng Rev 2006; 23:239-52. [DOI: 10.1080/02648725.2006.10648086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Abstract
Human respiratory syncytial virus (RSV) is the leading cause of paediatric respiratory disease and is the focus of antiviral- and vaccine-development programmes. These goals have been aided by an understanding of the virus genome architecture and the mechanisms by which it is expressed and replicated. RSV is a member of the order Mononegavirales and, as such, has a genome consisting of a single strand of negative-sense RNA. At first glance, transcription and genome replication appear straightforward, requiring self-contained promoter regions at the 3' ends of the genome and antigenome RNAs, short cis-acting elements flanking each of the genes and one polymerase. However, from these minimal elements, the virus is able to generate an array of capped, methylated and polyadenylated mRNAs and encapsidated antigenome and genome RNAs, all in the appropriate ratios to facilitate virus replication. The apparent simplicity of genome expression and replication is a consequence of considerable complexity in the polymerase structure and its cognate cis-acting sequences; here, our understanding of mechanisms by which the RSV polymerase proteins interact with signals in the RNA template to produce different RNA products is reviewed.
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MESH Headings
- Base Sequence
- DNA-Directed RNA Polymerases/metabolism
- Genome, Viral
- Humans
- Models, Biological
- Molecular Sequence Data
- Mononegavirales/genetics
- Mononegavirales/physiology
- Nucleocapsid/biosynthesis
- Nucleocapsid/genetics
- RNA, Antisense/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/pathogenicity
- Respiratory Syncytial Virus, Human/physiology
- Transcription, Genetic
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Vanessa M Cowton
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
| | - David R McGivern
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
| | - Rachel Fearns
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
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14
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Cowton VM, Fearns R. Evidence that the respiratory syncytial virus polymerase is recruited to nucleotides 1 to 11 at the 3' end of the nucleocapsid and can scan to access internal signals. J Virol 2005; 79:11311-22. [PMID: 16103183 PMCID: PMC1193587 DOI: 10.1128/jvi.79.17.11311-11322.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3'-terminal end of the respiratory syncytial virus genomic RNA contains a 44-nucleotide leader (Le) region adjoining the gene start signal of the first gene. Previous mapping studies demonstrated that there is a promoter located at the 3' end of Le, which can signal initiation of antigenome synthesis. The aim of this study was to investigate the role of the 3' terminus of the RNA template in (i) promoter recognition and (ii) determining the initiation site for antigenome synthesis. A panel of minigenomes containing additional sequence at the 3' end of the Le were analyzed for their ability to direct antigenome and mRNA synthesis. Minigenomes containing heterologous extensions of 6 nucleotides or more were unable to support efficient RNA synthesis. However, the activity of a minigenome with a 56-nucleotide extension could be restored by insertion of Le nucleotides 1 to 11 or 1 to 13 at the 3' end, indicating that these nucleotides, in conjunction with the 3' terminus, are sufficient to recruit polymerase to the template. Northern blot and 5' rapid amplification of cDNA ends analysis of antigenome RNA indicated that antigenome initiation occurred at the first position of Le, irrespective of the terminal extension. This finding demonstrates that the 3' terminus of the RNA is not necessary for determining the antigenome initiation site. Data are presented which suggest that following recruitment to a promoter at the 3' end of Le, the polymerase is able to scan and respond to a promoter signal embedded within the RNA template.
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Affiliation(s)
- Vanessa M Cowton
- Division of Pathology and Neuroscience, University of Dundee, UK
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