1
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Del Moral-Sánchez I, Wee EG, Xian Y, Lee WH, Allen JD, Torrents de la Peña A, Fróes Rocha R, Ferguson J, León AN, Koekkoek S, Schermer EE, Burger JA, Kumar S, Zwolsman R, Brinkkemper M, Aartse A, Eggink D, Han J, Yuan M, Crispin M, Ozorowski G, Ward AB, Wilson IA, Hanke T, Sliepen K, Sanders RW. Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines. NPJ Vaccines 2024; 9:74. [PMID: 38582771 PMCID: PMC10998906 DOI: 10.1038/s41541-024-00862-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/14/2024] [Indexed: 04/08/2024] Open
Abstract
Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.
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Affiliation(s)
- Iván Del Moral-Sánchez
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yuejiao Xian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebeca Fróes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - André N León
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Sanjeev Kumar
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Robby Zwolsman
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Aafke Aartse
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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2
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Devitt G, Johnson PB, Hanrahan N, Lane SIR, Vidale MC, Sheth B, Allen JD, Humbert MV, Spalluto CM, Hervé RC, Staples K, West JJ, Forster R, Divecha N, McCormick CJ, Crispin M, Hempler N, Malcolm GPA, Mahajan S. Mechanisms of SARS-CoV-2 Inactivation Using UVC Laser Radiation. ACS Photonics 2024; 11:42-52. [PMID: 38249683 PMCID: PMC10797618 DOI: 10.1021/acsphotonics.3c00828] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) has had a tremendous impact on humanity. Prevention of transmission by disinfection of surfaces and aerosols through a chemical-free method is highly desirable. Ultraviolet C (UVC) light is uniquely positioned to achieve inactivation of pathogens. We report the inactivation of SARS-CoV-2 virus by UVC radiation and explore its mechanisms. A dose of 50 mJ/cm2 using a UVC laser at 266 nm achieved an inactivation efficiency of 99.89%, while infectious virions were undetectable at 75 mJ/cm2 indicating >99.99% inactivation. Infection by SARS-CoV-2 involves viral entry mediated by the spike glycoprotein (S), and viral reproduction, reliant on translation of its genome. We demonstrate that UVC radiation damages ribonucleic acid (RNA) and provide in-depth characterization of UVC-induced damage of the S protein. We find that UVC severely impacts SARS-CoV- 2 spike protein's ability to bind human angiotensin-converting enzyme 2 (hACE2) and this correlates with loss of native protein conformation and aromatic amino acid integrity. This report has important implications for the design and development of rapid and effective disinfection systems against the SARS-CoV-2 virus and other pathogens.
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Affiliation(s)
- George Devitt
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Peter B. Johnson
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Simon I. R. Lane
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Magdalena C. Vidale
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bhavwanti Sheth
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Joel D. Allen
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Maria V. Humbert
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- University
of Cambridge, MRC Toxicology Unit, Cambridge, CB2 1QR, United Kingdom
| | - Cosma M. Spalluto
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- Southampton
NIHR Biomedical Research Centre, Southampton
General Hospital, Southampton SO16 6YD, United
Kingdom
| | - Rodolphe C. Hervé
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Karl Staples
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- Wessex Investigational
Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
- Southampton
NIHR Biomedical Research Centre, Southampton
General Hospital, Southampton SO16 6YD, United
Kingdom
| | - Jonathan J. West
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Cancer
Sciences, Faculty of Medicine, University
of Southampton, Southampton SO16 6YD, United
Kingdom
| | - Robert Forster
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Nullin Divecha
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Christopher J. McCormick
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
| | - Max Crispin
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Nils Hempler
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Graeme P. A. Malcolm
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Sumeet Mahajan
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Department
of Biotechnology, Inland Norway University
of Applied Sciences, Holsetgata 22, N-2317 Hamar, Norway
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3
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Newby ML, Allen JD, Crispin M. Influence of glycosylation on the immunogenicity and antigenicity of viral immunogens. Biotechnol Adv 2024; 70:108283. [PMID: 37972669 PMCID: PMC10867814 DOI: 10.1016/j.biotechadv.2023.108283] [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: 02/24/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
A key aspect of successful viral vaccine design is the elicitation of neutralizing antibodies targeting viral attachment and fusion glycoproteins that embellish viral particles. This observation has catalyzed the development of numerous viral glycoprotein mimetics as vaccines. Glycans can dominate the surface of viral glycoproteins and as such, the viral glycome can influence the antigenicity and immunogenicity of a candidate vaccine. In one extreme, glycans can form an integral part of epitopes targeted by neutralizing antibodies and are therefore considered to be an important feature of key immunogens within an immunization regimen. In the other extreme, the existence of peptide and bacterially expressed protein vaccines shows that viral glycosylation can be dispensable in some cases. However, native-like glycosylation can indicate native-like protein folding and the presence of conformational epitopes. Furthermore, going beyond native glycan mimicry, in either occupancy of glycosylation sites or the glycan processing state, may offer opportunities for enhancing the immunogenicity and associated protection elicited by an immunogen. Here, we review key determinants of viral glycosylation and how recombinant immunogens can recapitulate these signatures across a range of enveloped viruses, including HIV-1, Ebola virus, SARS-CoV-2, Influenza and Lassa virus. The emerging understanding of immunogen glycosylation and its control will help guide the development of future vaccines in both recombinant protein- and nucleic acid-based vaccine technologies.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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4
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Dadas O, Allen JD, Buchan SL, Kim J, Chan HTC, Mockridge CI, Duriez PJ, Rogel A, Crispin M, Al-Shamkhani A. Fcγ receptor binding is required for maximal immunostimulation by CD70-Fc. Front Immunol 2023; 14:1252274. [PMID: 37965342 PMCID: PMC10641686 DOI: 10.3389/fimmu.2023.1252274] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction T cell expressed CD27 provides costimulation upon binding to inducible membrane expressed trimeric CD70 and is required for protective CD8 T cell responses. CD27 agonists could therefore be used to bolster cellular vaccines and anti-tumour immune responses. To date, clinical development of CD27 agonists has focussed on anti-CD27 antibodies with little attention given to alternative approaches. Methods Here, we describe the generation and activity of soluble variants of CD70 that form either trimeric (t) or dimer-of-trimer proteins and conduct side-by-side comparisons with an agonist anti-CD27 antibody. To generate a dimer-of-trimer protein (dt), we fused three extracellular domains of CD70 to the Fc domain of mouse IgG1 in a 'string of beads' configuration (dtCD70-Fc). Results Whereas tCD70 failed to costimulate CD8 T cells, both dtCD70-Fc and an agonist anti-CD27 antibody were capable of enhancing T cell proliferation in vitro. Initial studies demonstrated that dtCD70-Fc was less efficacious than anti-CD27 in boosting a CD8 T cell vaccine response in vivo, concomitant with rapid clearance of dtCD70-Fc from the circulation. The accelerated plasma clearance of dtCD70-Fc was not due to the lack of neonatal Fc receptor binding but was dependent on the large population of oligomannose type glycosylation. Enzymatic treatment to reduce the oligomannose-type glycans in dtCD70-Fc improved its half-life and significantly enhanced its T cell stimulatory activity in vivo surpassing that of anti-CD27 antibody. We also show that whereas the ability of the anti-CD27 to boost a vaccine response was abolished in Fc gamma receptor (FcγR)-deficient mice, dtCD70-Fc remained active. By comparing the activity of dtCD70-Fc with a variant (dtCD70-Fc(D265A)) that lacks binding to FcγRs, we unexpectedly found that FcγR binding to dtCD70-Fc was required for maximal boosting of a CD8 T cell response in vivo. Interestingly, both dtCD70-Fc and dtCD70-Fc(D265A) were effective in prolonging the survival of mice harbouring BCL1 B cell lymphoma, demonstrating that a substantial part of the stimulatory activity of dtCD70-Fc in this setting is retained in the absence of FcγR interaction. Discussion These data reveal that TNFRSF ligands can be generated with a tunable activity profile and suggest that this class of immune agonists could have broad applications in immunotherapy.
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Affiliation(s)
- Osman Dadas
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, European University of Lefke, Lefke, Cyprus
| | - Joel D. Allen
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Sarah L. Buchan
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jinny Kim
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - H. T. Claude Chan
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - C. Ian Mockridge
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Patrick J. Duriez
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anne Rogel
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Max Crispin
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Aymen Al-Shamkhani
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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5
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Ringe RP, Colin P, Ozorowski G, Allen JD, Yasmeen A, Seabright GE, Lee JH, Antanasijevic A, Rantalainen K, Ketas T, Moore JP, Ward AB, Crispin M, Klasse PJ. Glycan heterogeneity as a cause of the persistent fraction in HIV-1 neutralization. PLoS Pathog 2023; 19:e1011601. [PMID: 37903160 PMCID: PMC10635575 DOI: 10.1371/journal.ppat.1011601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 08/07/2023] [Revised: 11/09/2023] [Accepted: 10/05/2023] [Indexed: 11/01/2023] Open
Abstract
Neutralizing antibodies (NAbs) to multiple epitopes on the HIV-1-envelope glycoprotein (Env) have been isolated from infected persons. The potency of NAbs is measured more often than the size of the persistent fraction of infectivity at maximum neutralization, which may also influence preventive efficacy of active or passive immunization and the therapeutic outcome of the latter. Many NAbs neutralize HIV-1 CZA97.012, a clone of a Clade-C isolate, to ~100%. But here NAb PGT151, directed to a fusion-peptide epitope, left a persistent fraction of 15%. NAb PGT145, ligating the Env-trimer apex, left no detectable persistent fraction. The divergence in persistent fractions was further analyzed by depletion of pseudoviral populations of the most PGT151- and PGT145-reactive virions. Thereby, neutralization by the non-depleting NAb increased, whereas neutralization by the depleting NAb decreased. Furthermore, depletion by PGT151 increased sensitivity to autologous neutralization by sera from rabbits immunized with soluble native-like CZA97.012 trimer: substantial persistent fractions were reduced. NAbs in these sera target epitopes comprising residue D411 at the V4-β19 transition in a defect of the glycan shield on CZA97.012 Env. NAb binding to affinity-fractionated soluble native-like CZA97.012 trimer differed commensurately with neutralization in analyses by ELISA and surface plasmon resonance. Glycan differences between PGT151- and PGT145-purified trimer fractions were then demonstrated by mass spectrometry, providing one explanation for the differential antigenicity. These differences were interpreted in relation to a new structure at 3.4-Å resolution of the soluble CZA97.012 trimer determined by cryo-electron microscopy. The trimer adopted a closed conformation, refuting apex opening as the cause of reduced PGT145 binding to the PGT151-purified form. The evidence suggests that differences in binding and neutralization after trimer purification or pseudovirus depletion with PGT145 or PGT151 are caused by variation in glycosylation, and that some glycan variants affect antigenicity through direct effects on antibody contacts, whereas others act allosterically.
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Affiliation(s)
- Rajesh P. Ringe
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Philippe Colin
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Gemma E. Seabright
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeong Hyun Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Ketas
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - P. J. Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
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6
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Cottrell CA, Pratap PP, Cirelli KM, Carnathan DG, Enemuo CA, Antanasijevic A, Ozorowski G, Sewall LM, Gao H, Greene KM, Allen JD, Ngo JT, Choe Y, Nogal B, Silva M, Bhiman J, Pauthner M, Irvine DJ, Montefiori D, Crispin M, Burton DR, Silvestri G, Crotty S, Ward AB. Focusing antibody responses to the fusion peptide in rhesus macaques. bioRxiv 2023:2023.06.26.545779. [PMID: 37425865 PMCID: PMC10327030 DOI: 10.1101/2023.06.26.545779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to elicit immune responses against the conserved fusion peptide. Antibody specificities and GC responses were tracked longitudinally using electron microscopy polyclonal epitope mapping (EMPEM) and lymph node fine-needle aspirates, respectively. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
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Affiliation(s)
- Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Payal P. Pratap
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kimberly M. Cirelli
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diane G. Carnathan
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Chiamaka A Enemuo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongmei Gao
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Kelli M. Greene
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julia T. Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Yury Choe
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Bartek Nogal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jinal Bhiman
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Darrell J. Irvine
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Montefiori
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dennis R. Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA02139, USA
| | - Guido Silvestri
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shane Crotty
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Division of Infectious Disease and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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7
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Allen JD, Ivory DP, Song SG, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses related to SARS-CoV-2. Cell Rep 2023; 42:112307. [PMID: 36972173 PMCID: PMC10015101 DOI: 10.1016/j.celrep.2023.112307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 08/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Vaccines remain successful at limiting severe disease and death, but the potential for further coronavirus zoonosis motivates the search for pan-coronavirus vaccines. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of 12 sarbecovirus glycan shields. Of the 22 N-linked glycan attachment sites present on SARS-CoV-2, 15 are shared by all 12 sarbecoviruses. However, there are significant differences in the processing state at glycan sites in the N-terminal domain, such as N165. Conversely, glycosylation sites in the S2 domain are highly conserved and contain a low abundance of oligomannose-type glycans, suggesting a low glycan shield density. The S2 domain may therefore provide a more attractive target for immunogen design efforts aiming to generate a pan-coronavirus antibody response.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Dylan P Ivory
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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8
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Caniels TG, Medina-Ramírez M, Zhang J, Sarkar A, Kumar S, LaBranche A, Derking R, Allen JD, Snitselaar JL, Capella-Pujol J, Sánchez IDM, Yasmeen A, Diaz M, Aldon Y, Bijl TPL, Venkatayogi S, Martin Beem JS, Newman A, Jiang C, Lee WH, Pater M, Burger JA, van Breemen MJ, de Taeye SW, Rantalainen K, LaBranche C, Saunders KO, Montefiori D, Ozorowski G, Ward AB, Crispin M, Moore JP, Klasse PJ, Haynes BF, Wilson IA, Wiehe K, Verkoczy L, Sanders RW. Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions. Cell Rep Med 2023; 4:101003. [PMID: 37044090 PMCID: PMC10140475 DOI: 10.1016/j.xcrm.2023.101003] [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: 09/15/2022] [Revised: 01/23/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.
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Affiliation(s)
- Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Max Medina-Ramírez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jinsong Zhang
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alex LaBranche
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Ronald Derking
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jonne L Snitselaar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Iván Del Moral Sánchez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Marilyn Diaz
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | | | | | - Amanda Newman
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Chuancang Jiang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Maarten Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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9
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Zhang YN, Paynter J, Antanasijevic A, Allen JD, Eldad M, Lee YZ, Copps J, Newby ML, He L, Chavez D, Frost P, Goodroe A, Dutton J, Lanford R, Chen C, Wilson IA, Crispin M, Ward AB, Zhu J. Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates. Nat Commun 2023; 14:1985. [PMID: 37031217 PMCID: PMC10082823 DOI: 10.1038/s41467-023-37742-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/10/2023] Open
Abstract
Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mor Eldad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Pat Frost
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Anna Goodroe
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - John Dutton
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Christopher Chen
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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10
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Margolin E, Schäfer G, Allen JD, Gers S, Woodward J, Sutherland AD, Blumenthal M, Meyers A, Shaw ML, Preiser W, Strasser R, Crispin M, Williamson AL, Rybicki EP, Chapman R. A plant-produced SARS-CoV-2 spike protein elicits heterologous immunity in hamsters. Front Plant Sci 2023; 14:1146234. [PMID: 36959936 PMCID: PMC10028082 DOI: 10.3389/fpls.2023.1146234] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/17/2023] [Indexed: 06/16/2023]
Abstract
Molecular farming of vaccines has been heralded as a cheap, safe and scalable production platform. In reality, however, differences in the plant biosynthetic machinery, compared to mammalian cells, can complicate the production of viral glycoproteins. Remodelling the secretory pathway presents an opportunity to support key post-translational modifications, and to tailor aspects of glycosylation and glycosylation-directed folding. In this study, we applied an integrated host and glyco-engineering approach, NXS/T Generation™, to produce a SARS-CoV-2 prefusion spike trimer in Nicotiana benthamiana as a model antigen from an emerging virus. The size exclusion-purified protein exhibited a characteristic prefusion structure when viewed by transmission electron microscopy, and this was indistinguishable from the equivalent mammalian cell-produced antigen. The plant-produced protein was decorated with under-processed oligomannose N-glycans and exhibited a site occupancy that was comparable to the equivalent protein produced in mammalian cell culture. Complex-type glycans were almost entirely absent from the plant-derived material, which contrasted against the predominantly mature, complex glycans that were observed on the mammalian cell culture-derived protein. The plant-derived antigen elicited neutralizing antibodies against both the matched Wuhan and heterologous Delta SARS-CoV-2 variants in immunized hamsters, although titres were lower than those induced by the comparator mammalian antigen. Animals vaccinated with the plant-derived antigen exhibited reduced viral loads following challenge, as well as significant protection from SARS-CoV-2 disease as evidenced by reduced lung pathology, lower viral loads and protection from weight loss. Nonetheless, animals immunized with the mammalian cell-culture-derived protein were better protected in this challenge model suggesting that more faithfully reproducing the native glycoprotein structure and associated glycosylation of the antigen may be desirable.
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Affiliation(s)
- Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Georgia Schäfer
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town, Cape Town, South Africa
| | - Joel D Allen
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Jeremy Woodward
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Andrew D Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town, South Africa
| | - Melissa Blumenthal
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Megan L Shaw
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town, South Africa
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Max Crispin
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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11
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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12
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Khan AO, Reyat JS, Hill H, Bourne JH, Colicchia M, Newby ML, Allen JD, Crispin M, Youd E, Murray PG, Taylor G, Stamataki Z, Richter AG, Cunningham AF, Pugh M, Rayes J. Preferential uptake of SARS-CoV-2 by pericytes potentiates vascular damage and permeability in an organoid model of the microvasculature. Cardiovasc Res 2022; 118:3085-3096. [PMID: 35709328 PMCID: PMC9214165 DOI: 10.1093/cvr/cvac097] [Citation(s) in RCA: 1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022] Open
Abstract
AIMS Thrombotic complications and vasculopathy have been extensively associated with severe COVID-19 infection; however, the mechanisms inducing endotheliitis and the disruption of endothelial integrity in the microcirculation are poorly understood. We hypothesized that within the vessel wall, pericytes preferentially take up viral particles and mediate the subsequent loss of vascular integrity. METHODS AND RESULTS Immunofluorescence of post-mortem patient sections was used to assess pathophysiological aspects of COVID-19 infection. The effects of COVID-19 on the microvasculature were assessed using a vascular organoid model exposed to live viral particles or recombinant viral antigens. We find increased expression of the viral entry receptor angiotensin-converting enzyme 2 on pericytes when compared to vascular endothelium and a reduction in the expression of the junctional protein CD144, as well as increased cell death, upon treatment with both live virus and/or viral antigens. We observe a dysregulation of genes implicated in vascular permeability, including Notch receptor 3, angiopoietin-2, and TEK. Activation of vascular organoids with interleukin-1β did not have an additive effect on vascular permeability. Spike antigen was detected in some patients' lung pericytes, which was associated with a decrease in CD144 expression and increased platelet recruitment and von Willebrand factor (VWF) deposition in the capillaries of these patients, with thrombi in large vessels rich in VWF and fibrin. CONCLUSION Together, our data indicate that direct viral exposure to the microvasculature modelled by organoid infection and viral antigen treatment results in pericyte infection, detachment, damage, and cell death, disrupting pericyte-endothelial cell crosstalk and increasing microvascular endothelial permeability, which can promote thrombotic and bleeding complications in the microcirculation.
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Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Jasmeet S Reyat
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Harriet Hill
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Joshua H Bourne
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Martina Colicchia
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Esther Youd
- Forensic Medicine and Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Paul G Murray
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
- Health Research Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Zania Stamataki
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Alex G Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthew Pugh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Julie Rayes
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
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13
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Willis JR, Berndsen ZT, Ma KM, Steichen JM, Schiffner T, Landais E, Liguori A, Kalyuzhniy O, Allen JD, Baboo S, Omorodion O, Diedrich JK, Hu X, Georgeson E, Phelps N, Eskandarzadeh S, Groschel B, Kubitz M, Adachi Y, Mullin TM, Alavi NB, Falcone S, Himansu S, Carfi A, Wilson IA, Yates JR, Paulson JC, Crispin M, Ward AB, Schief WR. Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors. Immunity 2022; 55:2149-2167.e9. [PMID: 36179689 PMCID: PMC9671094 DOI: 10.1016/j.immuni.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/12/2022] [Revised: 06/01/2022] [Accepted: 08/31/2022] [Indexed: 12/14/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.
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Affiliation(s)
- Jordan R Willis
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zachary T Berndsen
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Krystal M Ma
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jon M Steichen
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oluwarotimi Omorodion
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Xiaozhen Hu
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tina-Marie Mullin
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nushin B Alavi
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | - Ian A Wilson
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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14
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de la Peña AT, Sliepen K, Eshun-Wilson L, Newby ML, Allen JD, Zon I, Koekkoek S, Chumbe A, Crispin M, Schinkel J, Lander GC, Sanders RW, Ward AB. Structure of the hepatitis C virus E1E2 glycoprotein complex. Science 2022; 378:263-269. [PMID: 36264808 PMCID: PMC10512783 DOI: 10.1126/science.abn9884] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 11/02/2022]
Abstract
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope E1 and E2 glycoproteins are essential for viral entry and comprise the primary antigenic target for neutralizing antibody responses. The molecular mechanisms of E1E2 assembly, as well as how the E1E2 heterodimer binds broadly neutralizing antibodies, remain elusive. Here, we present the cryo-electron microscopy structure of the membrane-extracted full-length E1E2 heterodimer in complex with three broadly neutralizing antibodies-AR4A, AT1209, and IGH505-at ~3.5-angstrom resolution. We resolve the interface between the E1 and E2 ectodomains and deliver a blueprint for the rational design of vaccine immunogens and antiviral drugs.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Lisa Eshun-Wilson
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Gabriel C. Lander
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Andrew B. Ward
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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15
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Margolin E, Allen JD, Verbeek M, Chapman R, Meyers A, van Diepen M, Ximba P, Motlou T, Moore PL, Woodward J, Strasser R, Crispin M, Williamson AL, Rybicki EP. Augmenting glycosylation-directed folding pathways enhances the fidelity of HIV Env immunogen production in plants. Biotechnol Bioeng 2022; 119:2919-2937. [PMID: 35781691 PMCID: PMC9544252 DOI: 10.1002/bit.28169] [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: 04/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022]
Abstract
Heterologous glycoprotein production relies on host glycosylation-dependent folding. When the biosynthetic machinery differs from the usual expression host, there is scope to remodel the assembly pathway to enhance glycoprotein production. Here we explore the integration of chaperone coexpression with glyco-engineering to improve the production of a model HIV-1 envelope antigen. Calreticulin was coexpressed to support protein folding together with Leishmania major STT3D oligosaccharyltransferase, to improve glycan occupancy, RNA interference to suppress the formation of truncated glycans, and Nicotiana benthamiana plants lacking α1,3-fucosyltransferase and β1,2-xylosyltransferase was used as an expression host to prevent plant-specific complex N-glycans forming. This approach reduced the formation of undesired aggregates, which predominated in the absence of glyco-engineering. The resulting antigen also exhibited increased glycan occupancy, albeit to a slightly lower level than the equivalent mammalian cell-produced protein. The antigen was decorated almost exclusively with oligomannose glycans, which were less processed compared with the mammalian protein. Immunized rabbits developed comparable immune responses to the plant-produced and mammalian cell-derived antigens, including the induction of autologous neutralizing antibodies when the proteins were used to boost DNA and modified vaccinia Ankara virus-vectored vaccines. This study demonstrates that engineering glycosylation-directed folding offers a promising route to enhance the production of complex viral glycoproteins in plants.
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Affiliation(s)
- Emmanuel Margolin
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Matthew Verbeek
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Michiel van Diepen
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Phindile Ximba
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thopisang Motlou
- National Institute for Communicable Diseases of the National Health Laboratory Service, Centre for HIV and STIs, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Centre for HIV and STIs, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Jeremy Woodward
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Anna-Lise Williamson
- Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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16
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Zhao F, Berndsen ZT, Pedreño-Lopez N, Burns A, Allen JD, Barman S, Lee WH, Chakraborty S, Gnanakaran S, Sewall LM, Ozorowski G, Limbo O, Song G, Yong P, Callaghan S, Coppola J, Weisgrau KL, Lifson JD, Nedellec R, Voigt TB, Laurino F, Louw J, Rosen BC, Ricciardi M, Crispin M, Desrosiers RC, Rakasz EG, Watkins DI, Andrabi R, Ward AB, Burton DR, Sok D. Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun 2022; 13:5236. [PMID: 36068229 PMCID: PMC9446601 DOI: 10.1038/s41467-022-32783-2] [Citation(s) in RCA: 1] [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: 02/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.
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Affiliation(s)
- Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Zachary T Berndsen
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nuria Pedreño-Lopez
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Alison Burns
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Shawn Barman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Wen-Hsin Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Leigh M Sewall
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI, New York, NY, 10004, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jessica Coppola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kim L Weisgrau
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Thomas B Voigt
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Fernanda Laurino
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Johan Louw
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Brandon C Rosen
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Michael Ricciardi
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ronald C Desrosiers
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - David I Watkins
- Department of Pathology, George Washington University, Washington, DC, 20037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, 02139, USA.
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.
- IAVI, New York, NY, 10004, USA.
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17
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Allen JD, Ivory D, Ge Song S, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2. bioRxiv 2022:2022.08.24.505118. [PMID: 36052375 PMCID: PMC9435400 DOI: 10.1101/2022.08.24.505118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the impact of SARS-CoV-2. Vaccines remain successful at limiting severe disease and death, however the continued emergence of SARS-CoV-2 variants, together with the potential for further coronavirus zoonosis, motivates the search for pan-coronavirus vaccines that induce broadly neutralizing antibodies. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of several sarbecovirus glycan shields. Many N-linked glycan attachment sites are shared by all sarbecoviruses, and the processing state of certain sites is highly conserved. However, there are significant differences in the processing state at several glycan sites that surround the receptor binding domain. Our studies reveal similarities and differences in the glycosylation of sarbecoviruses and show how subtle changes in the protein sequence can have pronounced impacts on the glycan shield.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dylan Ivory
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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18
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Chawla H, Jossi SE, Faustini SE, Samsudin F, Allen JD, Watanabe Y, Newby ML, Marcial-Juárez E, Lamerton RE, McLellan JS, Bond PJ, Richter AG, Cunningham AF, Crispin M. Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic. J Mol Biol 2022; 434:167332. [PMID: 34717971 PMCID: PMC8550889 DOI: 10.1016/j.jmb.2021.167332] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 08/09/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023]
Abstract
Extensive glycosylation of viral glycoproteins is a key feature of the antigenic surface of viruses and yet glycan processing can also be influenced by the manner of their recombinant production. The low yields of the soluble form of the trimeric spike (S) glycoprotein from SARS-CoV-2 has prompted advances in protein engineering that have greatly enhanced the stability and yields of the glycoprotein. The latest expression-enhanced version of the spike incorporates six proline substitutions to stabilize the prefusion conformation (termed SARS-CoV-2 S HexaPro). Although the substitutions greatly enhanced expression whilst not compromising protein structure, the influence of these substitutions on glycan processing has not been explored. Here, we show that the site-specific N-linked glycosylation of the expression-enhanced HexaPro resembles that of an earlier version containing two proline substitutions (2P), and that both capture features of native viral glycosylation. However, there are site-specific differences in glycosylation of HexaPro when compared to 2P. Despite these discrepancies, analysis of the serological reactivity of clinical samples from infected individuals confirmed that both HexaPro and 2P protein are equally able to detect IgG, IgA, and IgM responses in all sera analysed. Moreover, we extend this observation to include an analysis of glycan engineered S protein, whereby all N-linked glycans were converted to oligomannose-type and conclude that serological activity is not impacted by large scale changes in glycosylation. These observations suggest that variations in glycan processing will not impact the serological assessments currently being performed across the globe.
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Affiliation(s)
- Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Sian E Faustini
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Edith Marcial-Juárez
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Rachel E Lamerton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Alex G Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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19
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Schorcht A, Cottrell CA, Pugach P, Ringe RP, Han AX, Allen JD, van den Kerkhof TLGM, Seabright GE, Schermer EE, Ketas TJ, Burger JA, van Schooten J, LaBranche CC, Ozorowski G, de Val N, Bader DLV, Schuitemaker H, Russell CA, Montefiori DC, van Gils MJ, Crispin M, Klasse PJ, Ward AB, Moore JP, Sanders RW. The Glycan Hole Area of HIV-1 Envelope Trimers Contributes Prominently to the Induction of Autologous Neutralization. J Virol 2022; 96:e0155221. [PMID: 34669426 PMCID: PMC8754230 DOI: 10.1128/jvi.01552-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) trimeric envelope glycoprotein (Env) is heavily glycosylated, creating a dense glycan shield that protects the underlying peptidic surface from antibody recognition. The absence of conserved glycans, due to missing potential N-linked glycosylation sites (PNGS), can result in strain-specific, autologous neutralizing antibody (NAb) responses. Here, we sought to gain a deeper understanding of the autologous neutralization by introducing holes in the otherwise dense glycan shields of the AMC011 and AMC016 SOSIP trimers. Specifically, when we knocked out the N130 and N289 glycans, which are absent from the well-characterized B41 SOSIP trimer, we observed stronger autologous NAb responses. We also analyzed the highly variable NAb responses induced in rabbits by diverse SOSIP trimers from subtypes A, B, and C. Statistical analysis, using linear regression, revealed that the cumulative area exposed on a trimer by glycan holes correlates with the magnitude of the autologous NAb response. IMPORTANCE Forty years after the first description of HIV-1, the search for a protective vaccine is still ongoing. The sole target for antibodies that can neutralize the virus are the trimeric envelope glycoproteins (Envs) located on the viral surface. The glycoprotein surface is covered with glycans that shield off the underlying protein components from recognition by the immune system. However, the Env trimers of some viral strains have holes in the glycan shield. Immunized animals developed antibodies against such glycan holes. These antibodies are generally strain specific. Here, we sought to gain a deeper understanding of what drives these specific immune responses. First, we show that strain-specific neutralizing antibody responses can be increased by creating artificial holes in the glycan shield. Second, when studying a diverse set of Env trimers with different characteristics, we found that the surface area of the glycan holes contributes prominently to the induction of strain-specific neutralizing antibodies.
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Affiliation(s)
- Anna Schorcht
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Pavel Pugach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rajesh P. Ringe
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Alvin X. Han
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Joel D. Allen
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Tom L. G. M. van den Kerkhof
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Gemma E. Seabright
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Edith E. Schermer
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas J. Ketas
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Judith A. Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Jelle van Schooten
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel L. V. Bader
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A. Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Max Crispin
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - P. J. Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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20
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Abstract
Understanding the glycosylation of the envelope spike (S) protein of SARS-CoV-2 is important in defining the antigenic surface of this key viral target. However, the underlying protein architecture may significantly influence glycan occupancy and processing. There is, therefore, potential for different recombinant fragments of S protein to display divergent glycosylation. Here, we show that the receptor binding domain (RBD), when expressed as a monomer, exhibits O-linked glycosylation, which is not recapitulated in the native-like soluble trimeric protein. We unambiguously assign O-linked glycosylation by homogenizing N-linked glycosylation using the enzymatic inhibitor, kifunensine, and then analyzing the resulting structures by electron-transfer higher-energy collision dissociation (EThcD) in an Orbitrap Eclipse Tribrid instrument. In the native-like trimer, we observe a single unambiguous O-linked glycan at T323, which displays very low occupancy. In contrast, several sites of O-linked glycosylation can be identified when RBD is expressed as a monomer, with T323 being almost completely occupied. We ascribe this effect to the relaxation of steric restraints arising from quaternary protein architecture. Our analytical approach has also highlighted that fragmentation ions arising from trace levels of truncated N-linked glycans can be misassigned as proximal putative O-linked glycan structures, particularly where a paucity of diagnostic fragments were obtained. Overall, we show that in matched expression systems the quaternary protein architecture limits O-linked glycosylation of the spike protein.
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Affiliation(s)
| | | | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
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21
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Chiodin G, Allen JD, Bryant DJ, Rock P, Martino EA, Valle-Argos B, Duriez PJ, Watanabe Y, Henderson I, Blachly JS, McCann KJ, Strefford JC, Packham G, Geijtenbeek TBH, Figdor CG, Wright GW, Staudt LM, Burack R, Bowden TA, Crispin M, Stevenson FK, Forconi F. Insertion of atypical glycans into the tumor antigen-binding site identifies DLBCLs with distinct origin and behavior. Blood 2021; 138:1570-1582. [PMID: 34424958 PMCID: PMC8554650 DOI: 10.1182/blood.2021012052] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Glycosylation of the surface immunoglobulin (Ig) variable region is a remarkable follicular lymphoma-associated feature rarely seen in normal B cells. Here, we define a subset of diffuse large B-cell lymphomas (DLBCLs) that acquire N-glycosylation sites selectively in the Ig complementarity-determining regions (CDRs) of the antigen-binding sites. Mass spectrometry and X-ray crystallography demonstrate how the inserted glycans are stalled at oligomannose-type structures because they are buried in the CDR loops. Acquisition of sites occurs in ∼50% of germinal-center B-cell-like DLBCL (GCB-DLBCL), mainly of the genetic EZB subtype, irrespective of IGHV-D-J use. This markedly contrasts with the activated B-cell-like DLBCL Ig, which rarely has sites in the CDR and does not seem to acquire oligomannose-type structures. Acquisition of CDR-located acceptor sites associates with mutations of epigenetic regulators and BCL2 translocations, indicating an origin shared with follicular lymphoma. Within the EZB subtype, these sites are associated with more rapid disease progression and with significant gene set enrichment of the B-cell receptor, PI3K/AKT/MTORC1 pathway, glucose metabolism, and MYC signaling pathways, particularly in the fraction devoid of MYC translocations. The oligomannose-type glycans on the lymphoma cells interact with the candidate lectin dendritic cell-specific intercellular adhesion molecule 3 grabbing non-integrin (DC-SIGN), mediating low-level signals, and lectin-expressing cells form clusters with lymphoma cells. Both clustering and signaling are inhibited by antibodies specifically targeting the DC-SIGN carbohydrate recognition domain. Oligomannosylation of the tumor Ig is a posttranslational modification that readily identifies a distinct GCB-DLBCL category with more aggressive clinical behavior, and it could be a potential precise therapeutic target via antibody-mediated inhibition of the tumor Ig interaction with DC-SIGN-expressing M2-polarized macrophages.
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Affiliation(s)
- Giorgia Chiodin
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Dean J Bryant
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Philip Rock
- Department of Pathology and Laboratory Medicine/Hematopathology, University of Rochester Medical Center, Rochester, NY
| | - Enrica A Martino
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
- Division of Hematology, Azienda Policlinico-Ospedale Vittorio Emanuele, University of Catania, Catania, Italy
| | - Beatriz Valle-Argos
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Patrick J Duriez
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Yasunori Watanabe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Isla Henderson
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - James S Blachly
- Division of Hematology, The Ohio State University, Columbus, OH
| | - Katy J McCann
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Jonathan C Strefford
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Graham Packham
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD; and
| | - Richard Burack
- Department of Pathology and Laboratory Medicine/Hematopathology, University of Rochester Medical Center, Rochester, NY
| | - Thomas A Bowden
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Freda K Stevenson
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
| | - Francesco Forconi
- School of Cancer Sciences, Cancer Research United Kingdom Southampton Centre, Faculty of Medicine
- Haematology Department, Cancer Care Directorate, University Hospital Southampton National Health Service Trust, Southampton, United Kingdom
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22
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Crooks ET, Almanza F, D’Addabbo A, Duggan E, Zhang J, Wagh K, Mou H, Allen JD, Thomas A, Osawa K, Korber BT, Tsybovsky Y, Cale E, Nolan J, Crispin M, Verkoczy LK, Binley JM. Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens. PLoS Pathog 2021; 17:e1009807. [PMID: 34679128 PMCID: PMC8565784 DOI: 10.1371/journal.ppat.1009807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/15/2021] [Revised: 11/03/2021] [Accepted: 10/07/2021] [Indexed: 02/07/2023] Open
Abstract
HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts. Despite almost 40 years of innovation, a vaccine to induce antibodies that block HIV infection remains elusive. Challenges include the unparalleled sequence diversity of HIV’s surface spikes and its dense sugar coat that limits antibody access. A growing number of monoclonal antibodies from HIV infected donors provide vaccine blueprints, but have been difficult to induce by vaccination, due to their unusual features. However, two targets, one at the viral spike apex and another at the side of the spikes are more forgiving in their ’demands’ for unusual antibodies. Here, we made a diverse panel of HIV spikes vulnerable at these two sites to be used as vaccines to try to focus antibodies on these targets. Our selection criteria for these spikes were: i) that when expressed on particles, they are infectious, allowing us to evaluate immunogens and vaccine sera using particles made with the same trimers, ii) that spikes are easy to produce by cells in quantities sufficient for vaccine use. Ultimately, we selected 7 trimers that will allow us to explore concepts that could bring us closer to an HIV vaccine.
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Affiliation(s)
- Emma T. Crooks
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Francisco Almanza
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Alessio D’Addabbo
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Erika Duggan
- Scintillon Institute, San Diego, California, United States of America
- Cellarcus BioSciences, La Jolla, California, United States of America
| | - Jinsong Zhang
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Kshitij Wagh
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Huihui Mou
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Alyssa Thomas
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Keiko Osawa
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Bette T. Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Yaroslav Tsybovsky
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Evan Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Nolan
- Scintillon Institute, San Diego, California, United States of America
- Cellarcus BioSciences, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Laurent K. Verkoczy
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - James M. Binley
- San Diego Biomedical Research Institute, San Diego, California, United States of America
- * E-mail:
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23
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Faustini SE, Jossi SE, Perez‐Toledo M, Shields AM, Allen JD, Watanabe Y, Newby ML, Cook A, Willcox CR, Salim M, Goodall M, Heaney JL, Marcial‐Juarez E, Morley GL, Torlinska B, Wraith DC, Veenith TV, Harding S, Jolles S, Ponsford MJ, Plant T, Huissoon A, O'Shea MK, Willcox BE, Drayson MT, Crispin M, Cunningham AF, Richter AG. Development of a high-sensitivity ELISA detecting IgG, IgA and IgM antibodies to the SARS-CoV-2 spike glycoprotein in serum and saliva. Immunology 2021; 164:135-147. [PMID: 33932228 PMCID: PMC8242512 DOI: 10.1111/imm.13349] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 11/19/2020] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Detecting antibody responses during and after SARS-CoV-2 infection is essential in determining the seroepidemiology of the virus and the potential role of antibody in disease. Scalable, sensitive and specific serological assays are essential to this process. The detection of antibody in hospitalized patients with severe disease has proven relatively straightforward; detecting responses in subjects with mild disease and asymptomatic infections has proven less reliable. We hypothesized that the suboptimal sensitivity of antibody assays and the compartmentalization of the antibody response may contribute to this effect. We systematically developed an ELISA, optimizing different antigens and amplification steps, in serum and saliva from non-hospitalized SARS-CoV-2-infected subjects. Using trimeric spike glycoprotein, rather than nucleocapsid, enabled detection of responses in individuals with low antibody responses. IgG1 and IgG3 predominate to both antigens, but more anti-spike IgG1 than IgG3 was detectable. All antigens were effective for detecting responses in hospitalized patients. Anti-spike IgG, IgA and IgM antibody responses were readily detectable in saliva from a minority of RT-PCR confirmed, non-hospitalized symptomatic individuals, and these were mostly subjects who had the highest levels of anti-spike serum antibodies. Therefore, detecting antibody responses in both saliva and serum can contribute to determining virus exposure and understanding immune responses after SARS-CoV-2 infection.
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Affiliation(s)
- Sian E. Faustini
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Sian E. Jossi
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | | | - Adrian M. Shields
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Joel D. Allen
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Yasunori Watanabe
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordUK
| | - Maddy L. Newby
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
| | | | - Carrie R. Willcox
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Mahboob Salim
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Margaret Goodall
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Jennifer L. Heaney
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | | | | | - Barbara Torlinska
- Institute of Applied Health ResearchUniversity of BirminghamBirminghamUK
| | - David C. Wraith
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Tonny V. Veenith
- Department of Critical Care MedicineUniversity Hospitals Birmingham NHS TrustBirminghamUK
| | | | | | | | - Tim Plant
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Aarnoud Huissoon
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
- Department of ImmunologyUniversity Hospitals Birmingham NHS Foundation TrustBirminghamUK
| | - Matthew K. O'Shea
- Institute of Microbiology and InfectionUniversity of BirminghamBirminghamUK
| | - Benjamin E. Willcox
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Mark T. Drayson
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Max Crispin
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Adam F. Cunningham
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Alex G. Richter
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
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24
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Shields AM, Faustini SE, Perez-Toledo M, Jossi S, Allen JD, Al-Taei S, Backhouse C, Dunbar LA, Ebanks D, Emmanuel B, Faniyi AA, Garvey M, Grinbergs A, McGinnell G, O'Neill J, Watanabe Y, Crispin M, Wraith DC, Cunningham AF, Drayson MT, Richter AG. Serological responses to SARS-CoV-2 following non-hospitalised infection: clinical and ethnodemographic features associated with the magnitude of the antibody response. BMJ Open Respir Res 2021; 8:e000872. [PMID: 34561239 PMCID: PMC8474079 DOI: 10.1136/bmjresp-2020-000872] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/30/2020] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To determine clinical and ethnodemographic correlates of serological responses against the SARS-CoV-2 spike glycoprotein following mild-to-moderate COVID-19. DESIGN A retrospective cohort study of healthcare workers who had self-isolated due to COVID-19. SETTING University Hospitals Birmingham NHS Foundation Trust, UK (UHBFT). PARTICIPANTS 956 healthcare workers were recruited by open invitation via UHBFT trust email and social media between 27 April 2020 and the 8 June 2020. INTERVENTION Participants volunteered a venous blood sample that was tested for the presence of anti-SARS-CoV-2 spike glycoprotein antibodies. Results were interpreted in the context of the symptoms of their original illness and ethnodemographic variables. RESULTS Using an assay that simultaneously measures the combined IgG, IgA and IgM response against the spike glycoprotein (IgGAM), the overall seroprevalence within this cohort was 46.2% (n=442/956). The seroprevalence of immunoglobulin isotypes was 36.3%, 18.7% and 8.1% for IgG, IgA and IgM, respectively. IgGAM identified serological responses in 40.6% (n=52/128) of symptomatic individuals who reported a negative SARS-CoV-2 PCR test. Increasing age, non-white ethnicity and obesity were independently associated with greater IgG antibody response against the spike glycoprotein. Self-reported fever and fatigue were associated with greater IgG and IgA responses against the spike glycoprotein. The combination of fever and/or cough and/or anosmia had a positive predictive value of 92.3% for seropositivity in self-isolating individuals a time when Wuhan strain SARS-CoV-2 was predominant. CONCLUSIONS AND RELEVANCE Assays employing combined antibody detection demonstrate enhanced seroepidemiological sensitivity and can detect prior viral exposure even when PCR swabs have been negative. We demonstrate an association between known ethnodemographic risk factors associated with mortality from COVID-19 and the magnitude of serological responses in mild-to-moderate disease.
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Affiliation(s)
- Adrian M Shields
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Sian E Faustini
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Marisol Perez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Sian Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Saly Al-Taei
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Claire Backhouse
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Lynsey A Dunbar
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Daniel Ebanks
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Beena Emmanuel
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Aduragbemi A Faniyi
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Mark Garvey
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Annabel Grinbergs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Golaleh McGinnell
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Joanne O'Neill
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - David C Wraith
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Adam F Cunningham
- MRC Centre for Immune Regulation, University of Birmingham, Birmingham, UK
| | - Mark T Drayson
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Alex G Richter
- Department of Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
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25
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Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Peña AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB. Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Nat Commun 2021; 12:4817. [PMID: 34376662 PMCID: PMC8355326 DOI: 10.1038/s41467-021-25087-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 02/26/2021] [Accepted: 07/23/2021] [Indexed: 11/08/2022] Open
Abstract
Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Leigh M Sewall
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Luis E Jimenez
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jennifer B Silverman
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jinal Bhiman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raiza Bastidas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jeffrey Copps
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hailee R Perrett
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Fabien Cannac
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuhe R Yang
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebeca Froes Rocha
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zachary T Berndsen
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil P King
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rogier W Sanders
- Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John P Moore
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Shane Crotty
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | | | - Dennis R Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew B Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
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26
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Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation. Biochemistry 2021; 60:2153-2169. [PMID: 34213308 PMCID: PMC8262170 DOI: 10.1021/acs.biochem.1c00279] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 04/27/2021] [Revised: 06/18/2021] [Indexed: 02/08/2023]
Abstract
A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.
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Affiliation(s)
- Joel D. Allen
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Himanshi Chawla
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Firdaus Samsudin
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
| | - Lorena Zuzic
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Chemistry, Faculty of Science and Engineering, Manchester Institute
of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K.
| | - Aishwary Tukaram Shivgan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Yasunori Watanabe
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Wan-ting He
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sean Callaghan
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ge Song
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peter Yong
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Philip J. M. Brouwer
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
| | - Yutong Song
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Yongfei Cai
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
| | - Helen M. E. Duyvesteyn
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Tomas Malinauskas
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
| | - Joeri Kint
- ExcellGene SA, CH1870 Monthey, Switzerland
| | - Paco Pino
- ExcellGene SA, CH1870 Monthey, Switzerland
| | | | - Martin Frank
- Biognos AB, Generatorsgatan
1, 41705 Göteborg, Sweden
| | - Bing Chen
- Division
of Molecular Medicine, Boston Children’s
Hospital, 3 Blackfan
Street, Boston, Massachusetts 02115, United States
- Department
of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts 02115, United States
| | - David I. Stuart
- Division
of Structural Biology, University of Oxford,
The Wellcome Centre for Human Genetics, Headington, Oxford OX3 7BN, U.K.
- Diamond Light Source Ltd., Harwell Science
& Innovation Campus, Didcot OX11 0DE, U.K.
| | - Rogier W. Sanders
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, Amsterdam Infection & Immunity Institute, 1007 MB Amsterdam, The Netherlands
- Department
of Microbiology and Immunology, Weill Medical
College of Cornell University, New York, New York 10065, United States
| | - Raiees Andrabi
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dennis R. Burton
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
- Consortium
for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California 92037, United States
- Ragon Institute of Massachusetts General
Hospital, Massachusetts
Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, United States
| | - Sai Li
- Tsinghua-Peking
Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing
Advanced Innovation Center for Structural Biology and Frontier Research
Center for Biological Structure, Beijing 100084, China
| | - Peter J. Bond
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore 138671
- Department
of Biological Sciences, National University
of Singapore, Singapore 117543
| | - Max Crispin
- School
of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
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27
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Hangartner L, Beauparlant D, Rakasz E, Nedellec R, Hozé N, McKenney K, Martins MA, Seabright GE, Allen JD, Weiler AM, Friedrich TC, Regoes RR, Crispin M, Burton DR. Effector function does not contribute to protection from virus challenge by a highly potent HIV broadly neutralizing antibody in nonhuman primates. Sci Transl Med 2021; 13:13/585/eabe3349. [PMID: 33731434 DOI: 10.1126/scitranslmed.abe3349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Accepted: 02/03/2021] [Indexed: 01/11/2023]
Abstract
Protection from immunodeficiency virus challenge in nonhuman primates (NHPs) by a first-generation HIV broadly neutralizing antibody (bnAb) b12 has previously been shown to benefit from interaction between the bnAb and Fcγ receptors (FcγRs) on immune cells. To investigate the mechanism of protection for a more potent second-generation bnAb currently in clinical trials, PGT121, we carried out a series of NHP studies. These studies included treating with PGT121 at a concentration at which only half of the animals were protected to avoid potential masking of FcγR effector function benefits by dominant neutralization and using a new variant that more completely eliminated all rhesus FcγR binding than earlier variants. In contrast to b12, which required FcγR binding for optimal protection, we concluded that PGT121-mediated protection is not augmented by FcγR interaction. Thus, for HIV-passive antibody prophylaxis, these results, together with existing literature, emphasize the importance of neutralization potency for clinical antibodies, with effector function requiring evaluation for individual antibodies.
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Affiliation(s)
- Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Beauparlant
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eva Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nathanaël Hozé
- Institute of Integrative Biology (IBZ), ETH Zurich, ETH Zentrum, CHN H76.2, Universitätstrasse 16, 8092 Zurich, Switzerland.,Theoretical Biology, ETH Zurich, ETH Zentrum, CHN K12.2, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mauricio A Martins
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - Roland R Regoes
- Institute of Integrative Biology (IBZ), ETH Zurich, ETH Zentrum, CHN H76.2, Universitätstrasse 16, 8092 Zurich, Switzerland.,Theoretical Biology, ETH Zurich, ETH Zentrum, CHN K12.2, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
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28
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Perez‐Toledo M, Faustini SE, Jossi SE, Shields AM, Marcial‐Juarez E, Kanthimathinathan HK, Allen JD, Watanabe Y, Goodall M, Willcox BE, Willcox CR, Salim M, Wraith DC, Veenith TV, Syrimi E, Drayson MT, Jyothish D, Al‐Abadi E, Chikermane A, Welch SB, Masilamani K, Hackett S, Crispin M, Scholefield BR, Cunningham AF, Richter AG. SARS-CoV-2-specific IgG1/IgG3 but not IgM in children with Pediatric Inflammatory Multi-System Syndrome. Pediatr Allergy Immunol 2021; 32:1125-1129. [PMID: 33724541 PMCID: PMC8250256 DOI: 10.1111/pai.13504] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022]
Affiliation(s)
| | - Sian E. Faustini
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Sian E. Jossi
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Adrian M. Shields
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | | | - Hari Krishnan Kanthimathinathan
- Birmingham Clinical Trials UnitUniversity of BirminghamBirminghamUK
- Paediatric Intensive Care UnitBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Joel D. Allen
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Yasunori Watanabe
- Oxford Glycobiology InstituteDepartment of BiochemistryUniversity of OxfordOxfordUK
| | - Margaret Goodall
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Benjamin E. Willcox
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Carrie R. Willcox
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Mahboob Salim
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - David C. Wraith
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Tonny V. Veenith
- Department of Critical Care MedicineUniversity Hospitals Birmingham NHS TrustBirminghamUK
| | - Eleni Syrimi
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Mark T. Drayson
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Deepthi Jyothish
- Department of General PaediatricsBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Eslam Al‐Abadi
- Birmingham Clinical Trials UnitUniversity of BirminghamBirminghamUK
- Childhood Arthritis and Rheumatic Diseases UnitBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Ashish Chikermane
- Department of CardiologyBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Steven B. Welch
- Department of PaediatricsBirmingham Chest Clinic and Heartlands HospitalUniversity Hospitals BirminghamBirminghamUK
| | - Kavitha Masilamani
- Department of General PaediatricsBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Scott Hackett
- West Midlands Immunodeficiency CentreHeartlands HospitalUniversity Hospitals BirminghamBirminghamUK
| | - Max Crispin
- School of Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Barnaby R. Scholefield
- Paediatric Intensive Care UnitBirmingham Women's and Children's NHS Foundation TrustBirminghamUK
- Institute of Inflammation and AgeingUniversity of BirminghamBirminghamUK
| | - Adam F. Cunningham
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Alex G. Richter
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
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29
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Kumar S, Lin X, Ngo T, Shapero B, Sou C, Allen JD, Copps J, Zhang L, Ozorowski G, He L, Crispin M, Ward AB, Wilson IA, Zhu J. Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. mBio 2021; 12:e0042921. [PMID: 34156262 PMCID: PMC8262854 DOI: 10.1128/mbio.00429-21] [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: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. IMPORTANCE Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response.
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Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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30
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Watanabe Y, Mendonça L, Allen ER, Howe A, Lee M, Allen JD, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska M, Belij-Rammerstorfer S, Morris S, Krebs AS, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton GR, Green CM, Lambe T, Zhang P, Gilbert SC, Crispin M. Native-like SARS-CoV-2 Spike Glycoprotein Expressed by ChAdOx1 nCoV-19/AZD1222 Vaccine. ACS Cent Sci 2021; 7:594-602. [PMID: 34056089 PMCID: PMC8043200 DOI: 10.1021/acscentsci.1c00080] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 05/08/2023]
Abstract
Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation, and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirm the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Affiliation(s)
- Yasunori Watanabe
- School
of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, U.K.
- Oxford
Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Luiza Mendonça
- Division
of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, U.K.
| | - Elizabeth R. Allen
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Andrew Howe
- Electron
Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, U.K.
| | - Mercede Lee
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Joel D. Allen
- School
of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, U.K.
| | - Himanshi Chawla
- School
of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, U.K.
| | - David Pulido
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Francesca Donnellan
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Hannah Davies
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Marta Ulaszewska
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Sandra Belij-Rammerstorfer
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
- NIHR Oxford
Biomedical Research Centre, Oxford, U.K.
| | - Susan Morris
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
| | - Anna-Sophia Krebs
- Division
of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, U.K.
| | - Wanwisa Dejnirattisai
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Juthathip Mongkolsapaya
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
- Dengue
Hemorrhagic Fever Research Unit, Office for Research and Development,
Faculty of Medicine, Siriraj Hospital, Mahidol
University, Bangkok, Thailand
- Chinese
Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, U.K.
| | - Piyada Supasa
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Gavin R. Screaton
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
- Division
of Medical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, U.K.
| | - Catherine M. Green
- The
Wellcome Centre for Human Genetics, University
of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Teresa Lambe
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
- NIHR Oxford
Biomedical Research Centre, Oxford, U.K.
| | - Peijun Zhang
- Division
of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, U.K.
- Electron
Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, U.K.
| | - Sarah C. Gilbert
- The
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
- NIHR Oxford
Biomedical Research Centre, Oxford, U.K.
| | - Max Crispin
- School
of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, U.K.
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31
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Derking R, Allen JD, Cottrell CA, Sliepen K, Seabright GE, Lee WH, Aldon Y, Rantalainen K, Antanasijevic A, Copps J, Yasmeen A, Cupo A, Cruz Portillo VM, Poniman M, Bol N, van der Woude P, de Taeye SW, van den Kerkhof TLGM, Klasse PJ, Ozorowski G, van Gils MJ, Moore JP, Ward AB, Crispin M, Sanders RW. Enhancing glycan occupancy of soluble HIV-1 envelope trimers to mimic the native viral spike. Cell Rep 2021; 35:108933. [PMID: 33826885 PMCID: PMC8804554 DOI: 10.1016/j.celrep.2021.108933] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 07/22/2020] [Revised: 12/10/2020] [Accepted: 03/11/2021] [Indexed: 12/31/2022] Open
Abstract
Artificial glycan holes on recombinant Env-based vaccines occur when a potential N-linked glycosylation site (PNGS) is under-occupied, but not on their viral counterparts. Native-like SOSIP trimers, including clinical candidates, contain such holes in the glycan shield that induce strain-specific neutralizing antibodies (NAbs) or non-NAbs. To eliminate glycan holes and mimic the glycosylation of native BG505 Env, we replace all 12 NxS sequons on BG505 SOSIP with NxT. All PNGS, except N133 and N160, are nearly fully occupied. Occupancy of the N133 site is increased by changing N133 to NxS, whereas occupancy of the N160 site is restored by reverting the nearby N156 sequon to NxS. Hence, PNGS in close proximity, such as in the N133-N137 and N156-N160 pairs, affect each other's occupancy. We further apply this approach to improve the occupancy of several Env strains. Increasing glycan occupancy should reduce off-target immune responses to vaccine antigens.
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Affiliation(s)
- Ronald Derking
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Victor M Cruz Portillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Niki Bol
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Patricia van der Woude
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - P J Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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32
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Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. Site-specific steric control of SARS-CoV-2 spike glycosylation. bioRxiv 2021:2021.03.08.433764. [PMID: 33758835 PMCID: PMC7986994 DOI: 10.1101/2021.03.08.433764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity between the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against infectious virus S protein. We find patterns which are conserved across all samples and this can be associated with site-specific stalling of glycan maturation which act as a highly sensitive reporter of protein structure. Molecular dynamics (MD) simulations of a fully glycosylated spike support s a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.
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33
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Brouwer PJM, Brinkkemper M, Maisonnasse P, Dereuddre-Bosquet N, Grobben M, Claireaux M, de Gast M, Marlin R, Chesnais V, Diry S, Allen JD, Watanabe Y, Giezen JM, Kerster G, Turner HL, van der Straten K, van der Linden CA, Aldon Y, Naninck T, Bontjer I, Burger JA, Poniman M, Mykytyn AZ, Okba NMA, Schermer EE, van Breemen MJ, Ravichandran R, Caniels TG, van Schooten J, Kahlaoui N, Contreras V, Lemaître J, Chapon C, Fang RHT, Villaudy J, Sliepen K, van der Velden YU, Haagmans BL, de Bree GJ, Ginoux E, Ward AB, Crispin M, King NP, van der Werf S, van Gils MJ, Le Grand R, Sanders RW. Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection. Cell 2021; 184:1188-1200.e19. [PMID: 33577765 PMCID: PMC7834972 DOI: 10.1016/j.cell.2021.01.035] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [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: 11/03/2020] [Revised: 12/23/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is continuing to disrupt personal lives, global healthcare systems, and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission, and disease. Here, we present a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-CoV-2 spike protein. Immunization studies show that this vaccine induces potent neutralizing antibody responses in mice, rabbits, and cynomolgus macaques. The vaccine-induced immunity protects macaques against a high-dose challenge, resulting in strongly reduced viral infection and replication in the upper and lower airways. These nanoparticles are a promising vaccine candidate to curtail the SARS-CoV-2 pandemic.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mathieu Claireaux
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | | | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Julia M Giezen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Gius Kerster
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karlijn van der Straten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Cynthia A van der Linden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marielle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Julien Lemaître
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Raphaël Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yme U van der Velden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, the Netherlands
| | - Eric Ginoux
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands.
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Lee CCD, Watanabe Y, Wu NC, Han J, Kumar S, Pholcharee T, Seabright GE, Allen JD, Lin CW, Yang JR, Liu MT, Wu CY, Ward AB, Crispin M, Wilson IA. A cross-neutralizing antibody between HIV-1 and influenza virus. PLoS Pathog 2021; 17:e1009407. [PMID: 33750987 PMCID: PMC8016226 DOI: 10.1371/journal.ppat.1009407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 09/21/2020] [Revised: 04/01/2021] [Accepted: 02/17/2021] [Indexed: 11/19/2022] Open
Abstract
Incessant antigenic evolution enables the persistence and spread of influenza virus in the human population. As the principal target of the immune response, the hemagglutinin (HA) surface antigen on influenza viruses continuously acquires and replaces N-linked glycosylation sites to shield immunogenic protein epitopes using host-derived glycans. Anti-glycan antibodies, such as 2G12, target the HIV-1 envelope protein (Env), which is even more extensively glycosylated and contains under-processed oligomannose-type clusters on its dense glycan shield. Here, we illustrate that 2G12 can also neutralize human seasonal influenza A H3N2 viruses that have evolved to present similar oligomannose-type clusters on their HAs from around 20 years after the 1968 pandemic. Using structural biology and mass spectrometric approaches, we find that two N-glycosylation sites close to the receptor binding site (RBS) on influenza hemagglutinin represent the oligomannose cluster recognized by 2G12. One of these glycan sites is highly conserved in all human H3N2 strains and the other emerged during virus evolution. These two N-glycosylation sites have also become crucial for fitness of recent H3N2 strains. These findings shed light on the evolution of the glycan shield on influenza virus and suggest 2G12-like antibodies can potentially act as broad neutralizers to target human enveloped viruses.
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Affiliation(s)
- Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, England, United Kingdom
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, England, United Kingdom
| | - Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tossapol Pholcharee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gemma E. Seabright
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, England, United Kingdom
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Chih-Wei Lin
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ji-Rong Yang
- Centers for Disease Control, Taipei City, Taiwan
| | | | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
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Allen JD, Watanabe Y, Chawla H, Newby ML, Crispin M. Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition. J Mol Biol 2021; 433:166762. [PMID: 33340519 PMCID: PMC7744274 DOI: 10.1016/j.jmb.2020.166762] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [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: 08/06/2020] [Revised: 11/03/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023]
Abstract
The severity of SARS-CoV-2 infection is highly variable and yet the molecular basis for this effect remains elusive. One potential contribution are differences in the glycosylation of target human cells, particularly as SARS-CoV-2 has the capacity to bind sialic acid which is a common, and highly variable, terminal modification of glycans. The viral spike glycoprotein (S) of SARS-CoV-2 and the human cellular receptor, angiotensin-converting enzyme 2 (ACE2) are both densely glycosylated. We therefore sought to investigate whether the glycosylation state of ACE2 impacts the interaction with SARS-CoV-2 viral spike. We generated a panel of engineered ACE2 glycoforms which were analyzed by mass spectrometry to reveal the site-specific glycan modifications. We then probed the impact of ACE2 glycosylation on S binding and revealed a subtle sensitivity with hypersialylated or oligomannose-type glycans slightly impeding the interaction. In contrast, deglycosylation of ACE2 did not influence SARS-CoV-2 binding. Overall, ACE2 glycosylation does not significantly influence viral spike binding. We suggest that any role of glycosylation in the pathobiology of SARS-CoV-2 will lie beyond its immediate impact of receptor glycosylation on virus binding.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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36
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Brouwer PJM, Antanasijevic A, de Gast M, Allen JD, Bijl TPL, Yasmeen A, Ravichandran R, Burger JA, Ozorowski G, Torres JL, LaBranche C, Montefiori DC, Ringe RP, van Gils MJ, Moore JP, Klasse PJ, Crispin M, King NP, Ward AB, Sanders RW. Immunofocusing and enhancing autologous Tier-2 HIV-1 neutralization by displaying Env trimers on two-component protein nanoparticles. NPJ Vaccines 2021; 6:24. [PMID: 33563983 PMCID: PMC7873233 DOI: 10.1038/s41541-021-00285-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 09/30/2020] [Accepted: 01/07/2021] [Indexed: 01/09/2023] Open
Abstract
The HIV-1 envelope glycoprotein trimer is poorly immunogenic because it is covered by a dense glycan shield. As a result, recombinant Env glycoproteins generally elicit inadequate antibody levels that neutralize clinically relevant, neutralization-resistant (Tier-2) HIV-1 strains. Multivalent antigen presentation on nanoparticles is an established strategy to increase vaccine-driven immune responses. However, due to nanoparticle instability in vivo, the display of non-native Env structures, and the inaccessibility of many neutralizing antibody (NAb) epitopes, the effects of nanoparticle display are generally modest for Env trimers. Here, we generate two-component self-assembling protein nanoparticles presenting twenty SOSIP trimers of the clade C Tier-2 genotype 16055. We show in a rabbit immunization study that these nanoparticles induce 60-fold higher autologous Tier-2 NAb titers than the corresponding SOSIP trimers. Epitope mapping studies reveal that the presentation of 16055 SOSIP trimers on these nanoparticle focuses antibody responses to an immunodominant apical epitope. Thus, these nanoparticles are a promising platform to improve the immunogenicity of Env trimers with apex-proximate NAb epitopes.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marlon de Gast
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Rajesh P Ringe
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
- Institute of Microbial Technology, Chandigarh, India
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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Watanabe Y, Mendonça L, Allen ER, Howe A, Lee M, Allen JD, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska M, Belij-Rammerstorfer S, Morris S, Krebs AS, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton GR, Green CM, Lambe T, Zhang P, Gilbert SC, Crispin M. Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine. bioRxiv 2021:2021.01.15.426463. [PMID: 33501433 PMCID: PMC7836103 DOI: 10.1101/2021.01.15.426463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Luiza Mendonça
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Elizabeth R. Allen
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Howe
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mercede Lee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - David Pulido
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Francesca Donnellan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Davies
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marta Ulaszewska
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sandra Belij-Rammerstorfer
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susan Morris
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna-Sophia Krebs
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Wanwisa Dejnirattisai
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Juthathip Mongkolsapaya
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Chinese Academy of Medical Science(CAMS) Oxford Institute (COI), University of Oxford, Oxford, U.K
| | - Piyada Supasa
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gavin R. Screaton
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Division of Medical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Catherine M. Green
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sarah C. Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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38
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Margolin E, Allen JD, Verbeek M, van Diepen M, Ximba P, Chapman R, Meyers A, Williamson AL, Crispin M, Rybicki E. Site-Specific Glycosylation of Recombinant Viral Glycoproteins Produced in Nicotiana benthamiana. Front Plant Sci 2021; 12:709344. [PMID: 34367227 PMCID: PMC8341435 DOI: 10.3389/fpls.2021.709344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/24/2021] [Indexed: 05/03/2023]
Abstract
There is an urgent need to establish large scale biopharmaceutical manufacturing capacity in Africa where the infrastructure for biologics production is severely limited. Molecular farming, whereby pharmaceuticals are produced in plants, offers a cheaper alternative to mainstream expression platforms, and is amenable to rapid large-scale production. However, there are several differences along the plant protein secretory pathway compared to mammalian systems, which constrain the production of complex pharmaceuticals. Viral envelope glycoproteins are important targets for immunization, yet in some cases they accumulate poorly in plants and may not be properly processed. Whilst the co-expression of human chaperones and furin proteases has shown promise, it is presently unclear how plant-specific differences in glycosylation impact the production of these proteins. In many cases it may be necessary to reproduce features of their native glycosylation to produce immunologically relevant vaccines, given that glycosylation is central to the folding and immunogenicity of these antigens. Building on previous work, we transiently expressed model glycoproteins from HIV and Marburg virus in Nicotiana benthamiana and mammalian cells. The proteins were purified and their site-specific glycosylation was determined by mass-spectrometry. Both glycoproteins yielded increased amounts of protein aggregates when produced in plants compared to the equivalent mammalian cell-derived proteins. The glycosylation profiles of the plant-produced glycoproteins were distinct from the mammalian cell produced proteins: they displayed lower levels of glycan occupancy, reduced complex glycans and large amounts of paucimannosidic structures. The elucidation of the site-specific glycosylation of viral glycoproteins produced in N. benthamiana is an important step toward producing heterologous viral glycoproteins in plants with authentic human-like glycosylation.
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Affiliation(s)
- Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
- *Correspondence: Emmanuel Margolin,
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Matthew Verbeek
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Michiel van Diepen
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Phindile Ximba
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rosamund Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Max Crispin,
| | - Edward Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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39
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Shields A, Faustini SE, Perez-Toledo M, Jossi S, Aldera E, Allen JD, Al-Taei S, Backhouse C, Bosworth A, Dunbar LA, Ebanks D, Emmanuel B, Garvey M, Gray J, Kidd IM, McGinnell G, McLoughlin DE, Morley G, O'Neill J, Papakonstantinou D, Pickles O, Poxon C, Richter M, Walker EM, Wanigasooriya K, Watanabe Y, Whalley C, Zielinska AE, Crispin M, Wraith DC, Beggs AD, Cunningham AF, Drayson MT, Richter AG. SARS-CoV-2 seroprevalence and asymptomatic viral carriage in healthcare workers: a cross-sectional study. Thorax 2020; 75:1089-1094. [PMID: 32917840 PMCID: PMC7462045 DOI: 10.1136/thoraxjnl-2020-215414] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [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: 05/27/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine the rates of asymptomatic viral carriage and seroprevalence of SARS-CoV-2 antibodies in healthcare workers. DESIGN A cross-sectional study of asymptomatic healthcare workers undertaken on 24/25 April 2020. SETTING University Hospitals Birmingham NHS Foundation Trust (UHBFT), UK. PARTICIPANTS 545 asymptomatic healthcare workers were recruited while at work. Participants were invited to participate via the UHBFT social media. Exclusion criteria included current symptoms consistent with COVID-19. No potential participants were excluded. INTERVENTION Participants volunteered a nasopharyngeal swab and a venous blood sample that were tested for SARS-CoV-2 RNA and anti-SARS-CoV-2 spike glycoprotein antibodies, respectively. Results were interpreted in the context of prior illnesses and the hospital departments in which participants worked. MAIN OUTCOME MEASURE Proportion of participants demonstrating infection and positive SARS-CoV-2 serology. RESULTS The point prevalence of SARS-CoV-2 viral carriage was 2.4% (n=13/545). The overall seroprevalence of SARS-CoV-2 antibodies was 24.4% (n=126/516). Participants who reported prior symptomatic illness had higher seroprevalence (37.5% vs 17.1%, χ2=21.1034, p<0.0001) and quantitatively greater antibody responses than those who had remained asymptomatic. Seroprevalence was greatest among those working in housekeeping (34.5%), acute medicine (33.3%) and general internal medicine (30.3%), with lower rates observed in participants working in intensive care (14.8%). BAME (Black, Asian and minority ethnic) ethnicity was associated with a significantly increased risk of seropositivity (OR: 1.92, 95% CI 1.14 to 3.23, p=0.01). Working on the intensive care unit was associated with a significantly lower risk of seropositivity compared with working in other areas of the hospital (OR: 0.28, 95% CI 0.09 to 0.78, p=0.02). CONCLUSIONS AND RELEVANCE We identify differences in the occupational risk of exposure to SARS-CoV-2 between hospital departments and confirm asymptomatic seroconversion occurs in healthcare workers. Further investigation of these observations is required to inform future infection control and occupational health practices.
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Affiliation(s)
- Adrian Shields
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Sian E Faustini
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Marisol Perez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Sian Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Erin Aldera
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Saly Al-Taei
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Claire Backhouse
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Andrew Bosworth
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lyndsey A Dunbar
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Daniel Ebanks
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Beena Emmanuel
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Mark Garvey
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Joanna Gray
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - I Michael Kidd
- Public Health England Midlands and East Region, Birmingham, UK
| | - Golaleh McGinnell
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Dee E McLoughlin
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Gabriella Morley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Joanna O'Neill
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Oliver Pickles
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Charlotte Poxon
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Megan Richter
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - Eloise M Walker
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kasun Wanigasooriya
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Celina Whalley
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - David C Wraith
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, NIHR Biomedical Research Centre, Birmingham, UK
| | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Mark T Drayson
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, NIHR Biomedical Research Centre, Birmingham, UK
| | - Alex G Richter
- Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
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Shields AM, Faustini SE, Perez-Toledo M, Jossi S, Allen JD, Al-Taei S, Backhouse C, Dunbar L, Ebanks D, Emmanuel B, Faniyi AA, Garvey MI, Grinbergs A, McGinnell G, O'Neill J, Watanabe Y, Crispin M, Wraith DC, Cunningham AF, Drayson MT, Richter AG. Serological responses to SARS-CoV-2 following non-hospitalised infection: clinical and ethnodemographic features associated with the magnitude of the antibody response. medRxiv 2020:2020.11.12.20230763. [PMID: 33236029 PMCID: PMC7685342 DOI: 10.1101/2020.11.12.20230763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To determine clinical and ethnodemographic correlates of serological responses against the SARS-CoV-2 spike glycoprotein following mild-to-moderate COVID-19. DESIGN A retrospective cohort study of healthcare workers who had self-isolated due to COVID-19. SETTING University Hospitals Birmingham NHS Foundation Trust, UK (UHBFT). PARTICIPANTS 956 health care workers were recruited by open invitation via UHBFT trust email and social media. INTERVENTION Participants volunteered a venous blood sample that was tested for the presence of anti-SARS-CoV-2 spike glycoprotein antibodies. Results were interpreted in the context of the symptoms of their original illness and ethnodemographic variables. RESULTS Using an assay that simultaneously measures the combined IgG, IgA and IgM response against the spike glycoprotein (IgGAM), the overall seroprevalence within this cohort was 46.2% (n=442/956). The seroprevalence of immunoglobulin isotypes was 36.3%, 18.7% and 8.1% for IgG, IgA and IgM respectively. IgGAM identified serological responses in 40.6% (n=52/128) of symptomatic individuals who reported a negative SARS-CoV-2 PCR test. Increasing age, non-white ethnicity and obesity were independently associated with greater IgG antibody response against the spike glycoprotein. Self-reported fever and fatigue were associated with greater IgG and IgA responses against the spike glycoprotein. The combination of fever and/or cough and/or anosmia had a positive predictive value of 92.3% for seropositivity. CONCLUSIONS AND RELEVANCE Assays employing combined antibody detection demonstrate enhanced seroepidemiological sensitivity and can detect prior viral exposure even when PCR swabs have been negative. We demonstrate an association between known ethnodemographic risk factors associated with mortality from COVID-19 and the magnitude of serological responses in mild-to-moderate disease. The combination of cough, and/or fever and/or anosmia identifies the majority of individuals who should self-isolate for COVID-19.
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Affiliation(s)
- Adrian M Shields
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
| | - Sian E Faustini
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Marisol Perez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Sian Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Saly Al-Taei
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Claire Backhouse
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Lynsey Dunbar
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Daniel Ebanks
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Beena Emmanuel
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
| | - Aduragbemi A Faniyi
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Mark I Garvey
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
| | - Annabel Grinbergs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
| | - Golaleh McGinnell
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
| | - Joanne O'Neill
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
| | - Yasunori Watanabe
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Max Crispin
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - David C Wraith
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, UK
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mark T Drayson
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, UK
| | - Alex G Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
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Morley GL, Taylor S, Jossi S, Perez-Toledo M, Faustini SE, Marcial-Juarez E, Shields AM, Goodall M, Allen JD, Watanabe Y, Newby ML, Crispin M, Drayson MT, Cunningham AF, Richter AG, O’Shea MK. Sensitive Detection of SARS-CoV-2-Specific Antibodies in Dried Blood Spot Samples. Emerg Infect Dis 2020; 26:2970-2973. [PMID: 32969788 PMCID: PMC7706975 DOI: 10.3201/eid2612.203309] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Dried blood spot (DBS) samples can be used for the detection of severe acute respiratory syndrome coronavirus 2 spike antibodies. DBS sampling is comparable to matched serum samples with a relative 98.1% sensitivity and 100% specificity. Thus, DBS sampling offers an alternative for population-wide serologic testing in the coronavirus pandemic.
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42
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Seabright GE, Cottrell CA, van Gils MJ, D'addabbo A, Harvey DJ, Behrens AJ, Allen JD, Watanabe Y, Scaringi N, Polveroni TM, Maker A, Vasiljevic S, de Val N, Sanders RW, Ward AB, Crispin M. Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions. Structure 2020; 28:897-909.e6. [PMID: 32433992 PMCID: PMC7416112 DOI: 10.1016/j.str.2020.04.022] [Citation(s) in RCA: 38] [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] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/27/2020] [Accepted: 04/28/2020] [Indexed: 11/22/2022]
Abstract
Numerous broadly neutralizing antibodies (bnAbs) have been identified that target the glycans of the HIV-1 envelope spike. Neutralization breadth is notable given that glycan processing can be substantially influenced by the presence or absence of neighboring glycans. Here, using a stabilized recombinant envelope trimer, we investigate the degree to which mutations in the glycan network surrounding an epitope impact the fine glycan processing of antibody targets. Using cryo-electron microscopy and site-specific glycan analysis, we reveal the importance of glycans in the formation of the 2G12 bnAb epitope and show that the epitope is only subtly impacted by variations in the glycan network. In contrast, we show that the PG9 and PG16 glycan-based epitopes at the trimer apex are dependent on the presence of the highly conserved surrounding glycans. Glycan networks underpin the conservation of bnAb epitopes and are an important parameter in immunogen design.
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Affiliation(s)
- Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Alessio D'addabbo
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - David J Harvey
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7FZ, UK
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Nicole Scaringi
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Thomas M Polveroni
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Allison Maker
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Snezana Vasiljevic
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Natalia de Val
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA; Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, AMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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Antanasijevic A, Ueda G, Brouwer PJM, Copps J, Huang D, Allen JD, Cottrell CA, Yasmeen A, Sewall LM, Bontjer I, Ketas TJ, Turner HL, Berndsen ZT, Montefiori DC, Klasse PJ, Crispin M, Nemazee D, Moore JP, Sanders RW, King NP, Baker D, Ward AB. Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens. PLoS Pathog 2020; 16:e1008665. [PMID: 32780770 PMCID: PMC7418955 DOI: 10.1371/journal.ppat.1008665] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 02/07/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and geometries enables combination with antigens of choice to test novel multimerization concepts in immunization strategies where the goal is to improve the induction and maturation of neutralizing antibody lineages. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to an underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. When the immunogenicity of ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle or as soluble proteins were compared in rabbits, the two immunogens elicited similar serum antibody binding titers against the trimer component. Neutralizing antibody titers were slightly elevated in the animals given the nanoparticle immunogen and were initially more focused to the trimer apex. Altogether, our findings indicate that tetrahedral nanoparticles can be successfully applied for presentation of HIV Env trimer immunogens; however, the optimal implementation to different immunization strategies remains to be determined.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
| | - George Ueda
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Jeffrey Copps
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
| | - Deli Huang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, United States of America
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Christopher A. Cottrell
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
| | - Anila Yasmeen
- Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Leigh M. Sewall
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
| | - Ilja Bontjer
- Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
| | - Thomas J. Ketas
- Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Hannah L. Turner
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
| | - Zachary T. Berndsen
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Per Johan Klasse
- Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - David Nemazee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, United States of America
| | - John P. Moore
- Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Rogier W. Sanders
- Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
| | - Neil P. King
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research, La Jolla, California, United States of America
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Abstract
The emergence of the betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), represents a considerable threat to global human health. Vaccine development is focused on the principal target of the humoral immune response, the spike (S) glycoprotein, which mediates cell entry and membrane fusion. The SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in protein folding and immune evasion. Here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant SARS-CoV-2 S immunogen. This analysis enables mapping of the glycan-processing states across the trimeric viral spike. We show how SARS-CoV-2 S glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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45
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Andrabi R, Pallesen J, Allen JD, Song G, Zhang J, de Val N, Gegg G, Porter K, Su CY, Pauthner M, Newman A, Bouton-Verville H, Garces F, Wilson IA, Crispin M, Hahn BH, Haynes BF, Verkoczy L, Ward AB, Burton DR. The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template. Cell Rep 2020; 27:2426-2441.e6. [PMID: 31116986 PMCID: PMC6533203 DOI: 10.1016/j.celrep.2019.04.082] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 09/24/2018] [Revised: 02/25/2019] [Accepted: 04/17/2019] [Indexed: 12/03/2022] Open
Abstract
Epitope-targeted HIV vaccine design seeks to focus antibody responses to broadly neutralizing antibody (bnAb) sites by sequential immunization. A chimpanzee simian immunodeficiency virus (SIV) envelope (Env) shares a single bnAb site, the variable loop 2 (V2)-apex, with HIV, suggesting its possible utility in an HIV immunization strategy. Here, we generate a chimpanzee SIV Env trimer, MT145K, which displays selective binding to HIV V2-apex bnAbs and precursor versions, but no binding to other HIV specificities. We determine the structure of the MT145K trimer by cryo-EM and show that its architecture is remarkably similar to HIV Env. Immunization of an HIV V2-apex bnAb precursor Ab-expressing knockin mouse with the chimpanzee MT145K trimer induces HIV V2-specific neutralizing responses. Subsequent boosting with an HIV trimer cocktail induces responses that exhibit some virus cross-neutralization. Overall, the chimpanzee MT145K trimer behaves as expected from design both in vitro and in vivo and is an attractive potential component of a sequential immunization regimen to induce V2-apex bnAbs. A designed chimpanzee SIV Env trimer binds HIV V2-apex bnAbs specifically The trimer (MT145K) is engineered to bind inferred unmutated versions of HIV V2-apex bnAbs The cryo-EM structure of the SIV MT145K trimer closely resembles that of HIV trimers The MT145K SIV trimer induces HIV-specific nAb responses in a favorable animal model
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Affiliation(s)
- Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesper Pallesen
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel D Allen
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; School of Biological Sciences, University of Southampton, Southampton, UK
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jinsong Zhang
- Duke Human Vaccine Institute and Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Natalia de Val
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gavin Gegg
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ching-Yao Su
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Newman
- Duke Human Vaccine Institute and Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hilary Bouton-Verville
- Duke Human Vaccine Institute and Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Fernando Garces
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; School of Biological Sciences, University of Southampton, Southampton, UK
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute and Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Duke Human Vaccine Institute and Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA; San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Andrew B Ward
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02114, USA.
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Faustini SE, Jossi SE, Perez-Toledo M, Shields AM, Allen JD, Watanabe Y, Newby ML, Cook A, Willcox CR, Salim M, Goodall M, Heaney JL, Marcial-Juarez E, Morley GL, Torlinska B, Wraith DC, Veenith TV, Harding S, Jolles S, Ponsford MJ, Plant T, Huissoon A, O'Shea MK, Willcox BE, Drayson MT, Crispin M, Cunningham AF, Richter AG. Detection of antibodies to the SARS-CoV-2 spike glycoprotein in both serum and saliva enhances detection of infection. medRxiv 2020:2020.06.16.20133025. [PMID: 32588002 PMCID: PMC7310662 DOI: 10.1101/2020.06.16.20133025] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Detecting antibody responses during and after SARS-CoV-2 infection is essential in determining the seroepidemiology of the virus and the potential role of antibody in disease. Scalable, sensitive and specific serological assays are essential to this process. The detection of antibody in hospitalized patients with severe disease has proven straightforward; detecting responses in subjects with mild disease and asymptomatic infections has proven less reliable. We hypothesized that the suboptimal sensitivity of antibody assays and the compartmentalization of the antibody response may contribute to this effect. METHODS We systemically developed an ELISA assay, optimising different antigens and amplification steps, in serum and saliva from symptomatic and asymptomatic SARS-CoV-2-infected subjects. RESULTS Using trimeric spike glycoprotein, rather than nucleocapsid enabled detection of responses in individuals with low antibody responses. IgG1 and IgG3 predominate to both antigens, but more anti-spike IgG1 than IgG3 was detectable. All antigens were effective for detecting responses in hospitalized patients. Anti-spike, but not nucleocapsid, IgG, IgA and IgM antibody responses were readily detectable in saliva from non-hospitalized symptomatic and asymptomatic individuals. Antibody responses in saliva and serum were largely independent of each other and symptom reporting. CONCLUSIONS Detecting antibody responses in both saliva and serum is optimal for determining virus exposure and understanding immune responses after SARS-CoV-2 infection. FUNDING This work was funded by the University of Birmingham, the National Institute for Health Research (UK), the NIH National Institute for Allergy and Infectious Diseases, the Bill and Melinda Gates Foundation and the University of Southampton.
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Affiliation(s)
- Sian E Faustini
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Marisol Perez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Adrian M Shields
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Alex Cook
- Binding Site Group Ltd, Birmingham, U.K
| | - Carrie R Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Mahboob Salim
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Margaret Goodall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Jennifer L Heaney
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Edith Marcial-Juarez
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Gabriella L Morley
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Barbara Torlinska
- Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - David C Wraith
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Tonny V Veenith
- Department of Critical Care Medicine, University Hospitals Birmingham NHS Trust, Birmingham, B15 2TH, U.K
| | | | | | | | - Tim Plant
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Aarnoud Huissoon
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, U.K
| | - Matthew K O'Shea
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Benjamin E Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Mark T Drayson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Alex G Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
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47
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Perez-Toledo M, Faustini SE, Jossi SE, Shields AM, Kanthimathinathan HK, Allen JD, Watanabe Y, Goodall M, Wraith DC, Veenith TV, Drayson MT, Jyothish D, Al-Abadi E, Chikermane A, Welch SB, Masilamani K, Hackett S, Crispin M, Scholefield BR, Cunningham AF, Richter AG. Serology confirms SARS-CoV-2 infection in PCR-negative children presenting with Paediatric Inflammatory Multi-System Syndrome. medRxiv 2020. [PMID: 32577677 PMCID: PMC7302282 DOI: 10.1101/2020.06.05.20123117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background During the COVID-19 outbreak, reports have surfaced of children who present with features of a multisystem inflammatory syndrome with overlapping features of Kawasaki disease and toxic shock syndrome - Paediatric Inflammatory Multisystem Syndrome- temporally associated with SARS-CoV-2 pandemic (PIMS-TS). Initial reports find that many of the children are PCR-negative for SARS-CoV-2, so it is difficult to confirm whether this syndrome is a late complication of viral infection in an age group largely spared the worst consequences of this infection, or if this syndrome reflects enhanced surveillance. Methods Children hospitalised for symptoms consistent with PIMS-TS between 28 April and 8 May 2020, and who were PCR-negative for SARS-CoV-2, were tested for antibodies to viral spike glycoprotein using an ELISA test. Results Eight patients (age range 7-14 years, 63% male) fulfilled case-definition for PIMS-TS during the study period. Six of the eight patients required admission to intensive care. All patients exhibited significant IgG and IgA responses to viral spike glycoprotein. Further assessment showed that the IgG isotypes detected in children with PIMS-TS were of the IgG1 and IgG3 subclasses, a distribution similar to that observed in samples from hospitalised adult COVID-19 patients. In contrast, IgG2 and IgG4 were not detected in children or adults. IgM was not detected in children, which contrasts with adult hospitalised adult COVID-19 patients of whom all had positive IgM responses. Conclusions Strong IgG antibody responses can be detected in PCR-negative children with PIMS-TS. The low detection rate of IgM in these patients is consistent with infection having occurred weeks previously and that the syndrome onset occurs well after the control of SARS-CoV-2 viral load. This implies that the disease is largely immune-mediated. Lastly, this indicates that serology can be an appropriate diagnostic tool in select patient groups.
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Affiliation(s)
- Marisol Perez-Toledo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Sian E Faustini
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Sian E Jossi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Adrian M Shields
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Hari Krishnan Kanthimathinathan
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, B15 2TT, U.K.,Paediatric Intensive Care Unit, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.,Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Margaret Goodall
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - David C Wraith
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Tonny V Veenith
- Department of Critical Care Medicine, University Hospitals Birmingham NHS Trust, Birmingham, B15 2TH, UK
| | - Mark T Drayson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Deepthi Jyothish
- Department of General Paediatrics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K
| | - Eslam Al-Abadi
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, B15 2TT, U.K.,Childhood Arthritis and Rheumatic Diseases Unit, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K
| | - Ashish Chikermane
- Department of Cardiology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K
| | - Steven B Welch
- Department of Paediatrics, Birmingham Chest Clinic and Heartlands Hospital, University Hospitals Birmingham, Birmingham, B9 5SS, U.K
| | - Kavitha Masilamani
- Department of General Paediatrics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K
| | - Scott Hackett
- West Midlands Immunodeficiency Centre, Heartlands Hospital, University Hospitals Birmingham, Birmingham, B9 5SS, U.K
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Barnaby R Scholefield
- Paediatric Intensive Care Unit, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, U.K.,Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Alex G Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K
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48
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Watanabe Y, Berndsen ZT, Raghwani J, Seabright GE, Allen JD, Pybus OG, McLellan JS, Wilson IA, Bowden TA, Ward AB, Crispin M. Vulnerabilities in coronavirus glycan shields despite extensive glycosylation. Nat Commun 2020; 11:2688. [PMID: 32461612 PMCID: PMC7253482 DOI: 10.1038/s41467-020-16567-0] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [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: 02/11/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. Vaccine development focuses on the principal target of the neutralizing humoral immune response, the spike (S) glycoprotein. Coronavirus S proteins are extensively glycosylated, encoding around 66-87 N-linked glycosylation sites per trimeric spike. Here, we reveal a specific area of high glycan density on MERS S that results in the formation of oligomannose-type glycan clusters, which were absent on SARS and HKU1 CoVs. We provide a comparison of the global glycan density of coronavirus spikes with other viral proteins including HIV-1 envelope, Lassa virus glycoprotein complex, and influenza hemagglutinin, where glycosylation plays a known role in shielding immunogenic epitopes. Overall, our data reveal how organisation of glycosylation across class I viral fusion proteins influence not only individual glycan compositions but also the immunological pressure across the protein surface.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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49
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Abstract
The emergence of the betacoronavirus, SARS-CoV-2 that causes COVID-19, represents a significant threat to global human health. Vaccine development is focused on the principal target of the humoral immune response, the spike (S) glycoprotein, that mediates cell entry and membrane fusion. SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in immune evasion and occluding immunogenic protein epitopes. Here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant SARS-CoV-2 S immunogen. This analysis enables mapping of the glycan-processing states across the trimeric viral spike. We show how SARS-CoV-2 S glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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50
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Brouwer PJM, Antanasijevic A, Berndsen Z, Yasmeen A, Fiala B, Bijl TPL, Bontjer I, Bale JB, Sheffler W, Allen JD, Schorcht A, Burger JA, Camacho M, Ellis D, Cottrell CA, Behrens AJ, Catalano M, Del Moral-Sánchez I, Ketas TJ, LaBranche C, van Gils MJ, Sliepen K, Stewart LJ, Crispin M, Montefiori DC, Baker D, Moore JP, Klasse PJ, Ward AB, King NP, Sanders RW. Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle. Nat Commun 2019; 10:4272. [PMID: 31537780 PMCID: PMC6753213 DOI: 10.1038/s41467-019-12080-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [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: 01/20/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity. Here we present the design and characterization of two-component protein NPs displaying 20 stabilized SOSIP trimers from various HIV-1 strains. The two-component nature permits the incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in vitro with high efficiency. Immunization studies show that the NPs are particularly efficacious as priming immunogens, improve the quality of the Ab response over a conventional one-component nanoparticle system, and are most effective when SOSIP trimers with an apex-proximate neutralizing epitope are displayed. Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.
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Affiliation(s)
- Philip J M Brouwer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Zachary Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Tom P L Bijl
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Jacob B Bale
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Arzeda Corporation, Seattle, Washington, 98119, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Joel D Allen
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Anna Schorcht
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Judith A Burger
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Miguel Camacho
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anna-Janina Behrens
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK.,New England Biolabs, Inc., Ipswich, Massachussetts, 01938, USA
| | - Marco Catalano
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Iván Del Moral-Sánchez
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Marit J van Gils
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Lance J Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Max Crispin
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.,Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98105, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.
| | - Rogier W Sanders
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
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