1
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Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024:101577. [PMID: 38761799 DOI: 10.1016/j.xcrm.2024.101577] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
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Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Hyllner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pia Dosenovic
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestraße 85, 22607 Hamburg, Germany.
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2
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Marking U, Bladh O, Aguilera K, Yang Y, Greilert Norin N, Blom K, Hober S, Klingström J, Havervall S, Åberg M, Sheward DJ, Thålin C. Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster in Sweden. Lancet Infect Dis 2024; 24:e80-e81. [PMID: 38190833 DOI: 10.1016/s1473-3099(23)00779-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Affiliation(s)
- Ulrika Marking
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden; Public Health Agency of Sweden, Sweden
| | - Oscar Bladh
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden
| | - Katherina Aguilera
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden
| | - Yiqiu Yang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nina Greilert Norin
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden
| | - Kim Blom
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden; Public Health Agency of Sweden, Sweden
| | - Sophia Hober
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden; Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonas Klingström
- Public Health Agency of Sweden, Sweden; Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sebastian Havervall
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden; Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mikael Åberg
- Department of Medical Sciences, Clinical Chemistry and SciLifeLab Affinity Proteomics, Uppsala University, Uppsala, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Thålin
- Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
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3
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Lenart K, Arcoverde Cerveira R, Hellgren F, Ols S, Sheward DJ, Kim C, Cagigi A, Gagne M, Davis B, Germosen D, Roy V, Alter G, Letscher H, Van Wassenhove J, Gros W, Gallouët AS, Le Grand R, Kleanthous H, Guebre-Xabier M, Murrell B, Patel N, Glenn G, Smith G, Loré K. Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2. NPJ Vaccines 2024; 9:17. [PMID: 38245545 PMCID: PMC10799869 DOI: 10.1038/s41541-024-00806-2] [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: 07/04/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024] Open
Abstract
The immune responses to Novavax's licensed NVX-CoV2373 nanoparticle Spike protein vaccine against SARS-CoV-2 remain incompletely understood. Here, we show in rhesus macaques that immunization with Matrix-MTM adjuvanted vaccines predominantly elicits immune events in local tissues with little spillover to the periphery. A third dose of an updated vaccine based on the Gamma (P.1) variant 7 months after two immunizations with licensed NVX-CoV2373 resulted in significant enhancement of anti-spike antibody titers and antibody breadth including neutralization of forward drift Omicron variants. The third immunization expanded the Spike-specific memory B cell pool, induced significant somatic hypermutation, and increased serum antibody avidity, indicating considerable affinity maturation. Seven months after immunization, vaccinated animals controlled infection by either WA-1 or P.1 strain, mediated by rapid anamnestic antibody and T cell responses in the lungs. In conclusion, a third immunization with an adjuvanted, low-dose recombinant protein vaccine significantly improved the quality of B cell responses, enhanced antibody breadth, and provided durable protection against SARS-CoV-2 challenge.
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Affiliation(s)
- Klara Lenart
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rodrigo Arcoverde Cerveira
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fredrika Hellgren
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Ols
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alberto Cagigi
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brandon Davis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Hélène Letscher
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Jérôme Van Wassenhove
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Wesley Gros
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Anne-Sophie Gallouët
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, Paris, France
| | - Harry Kleanthous
- Bill & Melinda Gates Foundation, Seattle, WA, USA
- SK Biosciences, Boston, MA, USA
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Karin Loré
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet, Stockholm, Sweden.
- Karolinska University Hospital, Stockholm, Sweden.
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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4
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Wall SC, Suryadevara N, Kim C, Shiakolas AR, Holt CM, Irbe EB, Wasdin PT, Suresh YP, Binshtein E, Chen EC, Zost SJ, Canfield E, Crowe JE, Thompson-Arildsen MA, Sheward DJ, Carnahan RH, Georgiev IS. SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes. Cell Rep Med 2023; 4:101267. [PMID: 37935199 PMCID: PMC10694659 DOI: 10.1016/j.xcrm.2023.101267] [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: 03/24/2023] [Revised: 07/17/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023]
Abstract
From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease compared with adults. Motivated by the established significance of SARS-CoV-2-neutralizing antibodies in adults, here we characterize SARS-CoV-2-specific antibody repertoires in a young cohort of individuals aged from 5 months to 18 years old. Our results show that neutralizing antibodies in children possess similar genetic features compared to antibodies identified in adults, with multiple antibodies from children belonging to previously established public antibody clonotypes in adults. Notably, antibodies from children show potent neutralization of circulating SARS-CoV-2 variants that have cumulatively resulted in resistance to virtually all approved monoclonal antibody therapeutics. Our results show that children can rely on similar SARS-CoV-2 antibody neutralization mechanisms compared to adults and are an underutilized source for the discovery of effective antibody therapeutics to counteract the ever-evolving pandemic.
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Affiliation(s)
- Steven C Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Andrea R Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Clinton M Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma B Irbe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Perry T Wasdin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yukthi P Suresh
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elaine C Chen
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth Canfield
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary Ann Thompson-Arildsen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Computer Science, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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5
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Sheward DJ, Yang Y, Westerberg M, Öling S, Muschiol S, Sato K, Peacock TP, Karlsson Hedestam GB, Albert J, Murrell B. Sensitivity of the SARS-CoV-2 BA.2.86 variant to prevailing neutralising antibody responses. Lancet Infect Dis 2023; 23:e462-e463. [PMID: 37776877 DOI: 10.1016/s1473-3099(23)00588-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023]
Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden.
| | - Yiqiu Yang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Michelle Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Sofia Öling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Sandra Muschiol
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK; The Pirbright Institute, Woking, UK
| | | | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
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6
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Roemer C, Sheward DJ, Hisner R, Gueli F, Sakaguchi H, Frohberg N, Schoenmakers J, Sato K, O'Toole Á, Rambaut A, Pybus OG, Ruis C, Murrell B, Peacock TP. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol 2023; 8:1952-1959. [PMID: 37845314 DOI: 10.1038/s41564-023-01504-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/28/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023]
Abstract
Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.
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Affiliation(s)
- Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ryan Hisner
- University of Cape Town, Rondebosch, South Africa
| | | | | | | | | | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK.
- The Pirbright Institute, Woking, UK.
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7
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Zhang J, Koolmeister C, Han J, Filograna R, Hanke L, Àdori M, Sheward DJ, Teifel S, Gopalakrishna S, Shao Q, Liu Y, Zhu K, Harris RA, McInerney G, Murrell B, Aoun M, Bäckdahl L, Holmdahl R, Pekalski M, Wedell A, Engvall M, Wredenberg A, Karlsson Hedestam GB, Castro Dopico X, Rorbach J. Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations. JCI Insight 2023; 8:e167656. [PMID: 37681412 PMCID: PMC10544217 DOI: 10.1172/jci.insight.167656] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/27/2023] [Indexed: 09/09/2023] Open
Abstract
Pathogenic mutations in mitochondrial (mt) tRNA genes that compromise oxidative phosphorylation (OXPHOS) exhibit heteroplasmy and cause a range of multisyndromic conditions. Although mitochondrial disease patients are known to suffer from abnormal immune responses, how heteroplasmic mtDNA mutations affect the immune system at the molecular level is largely unknown. Here, in mice carrying pathogenic C5024T in mt-tRNAAla and in patients with mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (MELAS) syndrome carrying A3243G in mt-tRNALeu, we found memory T and B cells to have lower pathogenic mtDNA mutation burdens than their antigen-inexperienced naive counterparts, including after vaccination. Pathogenic burden reduction was less pronounced in myeloid compared with lymphoid lineages, despite C5024T compromising macrophage OXPHOS capacity. Rapid dilution of the C5024T mutation in T and B cell cultures could be induced by antigen receptor-triggered proliferation and was accelerated by metabolic stress conditions. Furthermore, we found C5024T to dysregulate CD8+ T cell metabolic remodeling and IFN-γ production after activation. Together, our data illustrate that the generation of memory lymphocytes shapes the mtDNA landscape, wherein pathogenic variants dysregulate the immune response.
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Affiliation(s)
- Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jinming Han
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sina Teifel
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Qiuya Shao
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Keying Zhu
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Robert A. Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mike Aoun
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Liselotte Bäckdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Marcin Pekalski
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Wedell
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Engvall
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | | | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, and
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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8
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Vikström L, Fjällström P, Gwon YD, Sheward DJ, Wigren-Byström J, Evander M, Bladh O, Widerström M, Molnar C, Rasmussen G, Bennet L, Åberg M, Björk J, Tevell S, Thålin C, Blom K, Klingström J, Murrell B, Ahlm C, Normark J, Johansson AF, Forsell MNE. Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study. Lancet Reg Health Eur 2023:100646. [PMID: 37363799 PMCID: PMC10163377 DOI: 10.1016/j.lanepe.2023.100646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 06/28/2023]
Abstract
Background To inform future preventive measures including repeated vaccinations, we have searched for a clinically useful immune correlate of protection against fatal COVID-19 among nursing homes residents. Methods We performed repeated capillary blood sampling with analysis of S-binding IgG in an open cohort of nursing home residents in Sweden. We analyzed immunological and registry data from 16 September 2021 to 31 August 2022 with follow-up of deaths to 30 September 2022. The study period included implementation of the 3rd and 4th mRNA monovalent vaccine doses and Omicron virus waves. Findings A total of 3012 nursing home residents with median age 86 were enrolled. The 3rd mRNA dose elicited a 99-fold relative increase of S-binding IgG in blood and corresponding increase of neutralizing antibodies. The 4th mRNA vaccine dose boosted levels 3.8-fold. Half-life of S-binding IgG was 72 days. A total 528 residents acquired their first SARS-CoV-2 infection after the 3rd or the 4th vaccine dose and the associated 30-day mortality was 9.1%. We found no indication that levels of vaccine-induced antibodies protected against infection with Omicron VOCs. In contrast, the risk of death was inversely correlated to levels of S-directed IgG below the 20th percentile. The death risk plateaued at population average above the lower 35th percentile of S-binding IgG. Interpretation In the absence of neutralizing antibodies that protect from infection, quantification of S-binding IgG post vaccination may be useful to identify the most vulnerable for fatal COVID-19 among the oldest and frailest. This information is of importance for future strategies to protect vulnerable populations against neutralization resistant variants of concern. Funding Swedish Research Council, SciLifeLab via Knut and Alice Wallenberg Foundation, VINNOVA. Swedish Healthcare Regions, and Erling Persson Foundation.
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Affiliation(s)
- Linnea Vikström
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Peter Fjällström
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Yong-Dae Gwon
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Daniel J Sheward
- The Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | | | - Magnus Evander
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Oscar Bladh
- The Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden
| | - Micael Widerström
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | | | | | - Louise Bennet
- Department of Clinical Sciences, Clinical Studies Sweden, Forum South, Skåne University Hospital, Lund University, Lund, Sweden
| | - Mikael Åberg
- The Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jonas Björk
- The Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Staffan Tevell
- Faculty of Medicine and Health, The Department of Infectious Diseases, Karlstad Hospital and Centre for Clinical Research and Education, Region Värmland, Örebro University, Örebro, Sweden
| | - Charlotte Thålin
- The Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden
| | - Kim Blom
- The Swedish Public Health Agency, Stockholm, Sweden
| | - Jonas Klingström
- The Department of Biomedical Clinical Sciences, Linköpings University, Linköping, Sweden
| | - Ben Murrell
- The Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Clas Ahlm
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Johan Normark
- The Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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9
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Chernyshev M, Sakharkar M, Connor RI, Dugan HL, Sheward DJ, Rappazzo CG, Stålmarck A, Forsell MNE, Wright PF, Corcoran M, Murrell B, Walker LM, Karlsson Hedestam GB. Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages. Nat Commun 2023; 14:2249. [PMID: 37076511 PMCID: PMC10115384 DOI: 10.1038/s41467-023-37972-1] [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: 11/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Vaccination of SARS-CoV-2 convalescent individuals generates broad and potent antibody responses. Here, we isolate 459 spike-specific monoclonal antibodies (mAbs) from two individuals who were infected with the index variant of SARS-CoV-2 and later boosted with mRNA-1273. We characterize mAb genetic features by sequence assignments to the donors' personal immunoglobulin genotypes and assess antibody neutralizing activities against index SARS-CoV-2, Beta, Delta, and Omicron variants. The mAbs used a broad range of immunoglobulin heavy chain (IGH) V genes in the response to all sub-determinants of the spike examined, with similar characteristics observed in both donors. IGH repertoire sequencing and B cell lineage tracing at longitudinal time points reveals extensive evolution of SARS-CoV-2 spike-binding antibodies from acute infection until vaccination five months later. These results demonstrate that highly polyclonal repertoires of affinity-matured memory B cells are efficiently recalled by vaccination, providing a basis for the potent antibody responses observed in convalescent persons following vaccination.
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Affiliation(s)
- Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ruth I Connor
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Peter F Wright
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura M Walker
- Adimab LLC, Lebanon, NH, 03766, USA.
- Invivyd Inc, Waltham, MA, 02451, USA.
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10
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Pushparaj P, Nicoletto A, Castro Dopico X, Sheward DJ, Kim S, Ekström S, Murrell B, Corcoran M, Karlsson Hedestam GB. Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses. Front Virol 2023; 3:1128253. [PMID: 37041983 PMCID: PMC7614418 DOI: 10.3389/fviro.2023.1128253] [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: 03/08/2023]
Abstract
The antibody response to SARS-CoV-2 shows biased immunoglobulin heavy chain variable (IGHV) gene usage, allowing definition of genetic signatures for some classes of neutralizing antibodies. We investigated IGHV gene usage frequencies by sorting spike-specific single memory B cells from individuals infected with SARS-CoV-2 early in the pandemic. From two study participants and 703 spike-specific B cells, the most used genes were IGHV1-69, IGHV3-30-3, and IGHV3-30. Here, we focused on the IGHV3-30 group of genes and an IGHV3-30-3-using ultrapotent neutralizing monoclonal antibody, CAB-F52, which displayed broad neutralizing activity also in its germline-reverted form. IGHV3-30-3 is encoded by a region of the IGH locus that is highly variable at both the allelic and structural levels. Using personalized IG genotyping, we found that 4 of 14 study participants lacked the IGHV3-30-3 gene on both chromosomes, raising the question if other, highly similar IGHV genes could substitute for IGHV3-30-3 in persons lacking this gene. In the context of CAB-F52, we found that none of the tested IGHV3-33 alleles, but several IGHV3-30 alleles could substitute for IGHV3-30-3, suggesting functional redundancy between the highly homologous IGHV3-30 and IGHV3-30-3 genes for this antibody.
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Affiliation(s)
- Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Nicoletto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Simon Ekström
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla B. Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- CORRESPONDENCE Gunilla B. Karlsson Hedestam
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11
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Christensen D, Polacek C, Sheward DJ, Hanke L, McInerney G, Murrell B, Hartmann KT, Jensen HE, Zimmermann J, Jungersen G, Illigen KE, Isling LK, Fernandez-Antunez C, Ramirez S, Bukh J, Pedersen GK. SARS-CoV-2 spike HexaPro formulated in aluminium hydroxide and administered in an accelerated vaccination schedule partially protects Syrian Hamsters against viral challenge despite low neutralizing antibody responses. Front Immunol 2023; 14:941281. [PMID: 36756130 PMCID: PMC9900178 DOI: 10.3389/fimmu.2023.941281] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2 continues to pose a threat to human health as new variants emerge and thus a diverse vaccine pipeline is needed. We evaluated SARS-CoV-2 HexaPro spike protein formulated in Alhydrogel® (aluminium oxyhydroxide) in Syrian hamsters, using an accelerated two dose regimen (given 10 days apart) and a standard regimen (two doses given 21 days apart). Both regimens elicited spike- and RBD-specific IgG antibody responses of similar magnitude, but in vitro virus neutralization was low or undetectable. Despite this, the accelerated two dose regimen offered reduction in viral load and protected against lung pathology upon challenge with homologous SARS-CoV-2 virus (Wuhan-Hu-1). This highlights that vaccine-induced protection against SARS-CoV-2 disease can be obtained despite low neutralizing antibody levels and suggests that accelerated vaccine schedules may be used to confer rapid protection against SARS-CoV-2 disease.
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Affiliation(s)
- Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus Research and Development Laboratory, Department of Microbial Diagnostic and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Katrine Top Hartmann
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Zimmermann
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Gregers Jungersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Louise Krag Isling
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Kristian Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark,*Correspondence: Gabriel Kristian Pedersen,
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12
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Scharf L, Axelsson H, Emmanouilidi A, Mathew NR, Sheward DJ, Leach S, Isakson P, Smirnov IV, Marklund E, Miron N, Andersson LM, Gisslén M, Murrell B, Lundgren A, Bemark M, Angeletti D. Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones. JCI Insight 2023; 8:165299. [PMID: 36445762 PMCID: PMC9870078 DOI: 10.1172/jci.insight.165299] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from patients with severe COVID-19 every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single-cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and B cell receptor-Seq (BCR-Seq) with oligo-tagged antigen baits. While the proportion of Spike receptor binding domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike- and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen-specific cells, and affinity maturation was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to 1 year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen-specific B cell responses in longitudinally sampled patients infected with COVID-19.
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Affiliation(s)
- Lydia Scharf
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hannes Axelsson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Aikaterini Emmanouilidi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nimitha R. Mathew
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Susannah Leach
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pharmacology
| | - Pauline Isakson
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Ilya V. Smirnov
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Emelie Marklund
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nicolae Miron
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lundgren
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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13
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Gupta G, Hamawandi B, Sheward DJ, Murrell B, Hanke L, McInerney G, Blosi M, Costa AL, Toprak MS, Fadeel B. Silver nanoparticles with excellent biocompatibility block pseudotyped SARS-CoV-2 in the presence of lung surfactant. Front Bioeng Biotechnol 2022; 10:1083232. [PMID: 36578508 PMCID: PMC9790969 DOI: 10.3389/fbioe.2022.1083232] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Silver (Ag) is known to possess antimicrobial properties which is commonly attributed to soluble Ag ions. Here, we showed that Ag nanoparticles (NPs) potently inhibited SARS-CoV-2 infection using two different pseudovirus neutralization assays. We also evaluated a set of Ag nanoparticles of different sizes with varying surface properties, including polyvinylpyrrolidone (PVP)-coated and poly (ethylene glycol) (PEG)-modified Ag nanoparticles, and found that only the bare (unmodified) nanoparticles were able to prevent virus infection. For comparison, TiO2 nanoparticles failed to intercept the virus. Proteins and lipids may adsorb to nanoparticles forming a so-called bio-corona; however, Ag nanoparticles pre-incubated with pulmonary surfactant retained their ability to block virus infection in the present model. Furthermore, the secondary structure of the spike protein of SARS-CoV-2 was perturbed by the Ag nanoparticles, but not by the ionic control (AgNO3) nor by the TiO2 nanoparticles. Finally, Ag nanoparticles were shown to be non-cytotoxic towards the human lung epithelial cell line BEAS-2B and this was confirmed by using primary human nasal epithelial cells. These results further support that Ag nanoparticles may find use as anti-viral agents.
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Affiliation(s)
- Govind Gupta
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bejan Hamawandi
- Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Magda Blosi
- Institute of Science and Technology for Ceramics, National Research Council of Italy, Faenza, Italy
| | - Anna L. Costa
- Institute of Science and Technology for Ceramics, National Research Council of Italy, Faenza, Italy
| | - Muhammet S. Toprak
- Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden,*Correspondence: Bengt Fadeel,
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14
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Sheward DJ, Kim C, Fischbach J, Sato K, Muschiol S, Ehling RA, Björkström NK, Hedestam GBK, Reddy ST, Albert J, Peacock TP, Murrell B. Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies. Lancet Infect Dis 2022; 22:1538-1540. [PMID: 36244347 PMCID: PMC9560757 DOI: 10.1016/s1473-3099(22)00663-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Sandra Muschiol
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
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15
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Sheward DJ, Kim C, Fischbach J, Muschiol S, Ehling RA, Björkström NK, Karlsson Hedestam GB, Reddy ST, Albert J, Peacock TP, Murrell B. Evasion of neutralising antibodies by omicron sublineage BA.2.75. Lancet Infect Dis 2022; 22:1421-1422. [PMID: 36058228 PMCID: PMC9436366 DOI: 10.1016/s1473-3099(22)00524-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Sandra Muschiol
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden.
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16
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Christensen D, Polacek C, Sheward DJ, Hanke L, Moliner-Morro A, McInerney G, Murrell B, Hartmann KT, Jensen HE, Jungersen G, Illigen K, Isling LK, Jensen RF, Hansen JS, Rosenkrands I, Fernandez-Antunez C, Ramirez S, Follmann F, Bukh J, Pedersen GK. Protection against SARS-CoV-2 transmission by a parenteral prime—Intranasal boost vaccine strategy. EBioMedicine 2022; 84:104248. [PMID: 36088218 PMCID: PMC9448948 DOI: 10.1016/j.ebiom.2022.104248] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Background Licensed vaccines against SARS-CoV-2 effectively protect against severe disease, but display incomplete protection against virus transmission. Mucosal vaccines providing immune responses in the upper airways are one strategy to protect against transmission. Methods We administered Spike HexaPro trimer formulated in a cationic liposomal adjuvant as a parenteral (subcutaneous – s.c.) prime - intranasal boost regimen to elicit airway mucosal immune responses and evaluated this in a Syrian hamster model of virus transmission. Findings Parenteral prime - intranasal boost elicited high-magnitude serum neutralizing antibody responses and IgA responses in the upper respiratory tract. The vaccine strategy protected against virus in the lower airways and lung pathology, but virus could still be detected in the upper airways. Despite this, the parenteral prime - intranasal booster vaccine effectively protected against onward SARS-CoV-2 transmission. Interpretation This study suggests that parenteral-prime mucosal boost is an effective strategy for protecting against SARS-CoV-2 infection and highlights that protection against virus transmission may be obtained despite incomplete clearance of virus from the upper respiratory tract. It should be noted that protection against onward transmission was not compared to standard parenteral prime-boost, which should be a focus for future studies. Funding This work was primarily supported by the European Union Horizon 2020 research and innovation program under grant agreement no. 101003653.
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Affiliation(s)
- Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus Research & Development Laboratory, Department of Virology and Microbiological Special diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Katrine Top Hartmann
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen Denmark
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen Denmark
| | - Gregers Jungersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Kristin Illigen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Krag Isling
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Julia Sid Hansen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ida Rosenkrands
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Follmann
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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17
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Sheward DJ, Hermanus T, Murrell B, Garrett N, Abdool Karim SS, Morris L, Moore PL, Williamson C. HIV Coinfection Provides Insights for the Design of Vaccine Cocktails to Elicit Broadly Neutralizing Antibodies. J Virol 2022; 96:e0032422. [PMID: 35758668 PMCID: PMC9327685 DOI: 10.1128/jvi.00324-22] [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: 02/19/2022] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
Induction of broadly neutralizing antibodies (bNAbs) to HIV and other diverse pathogens will likely require the use of multiple immunogens. An understanding of the dynamics of antibody development to multiple diverse but related antigens would facilitate the rational design of immunization strategies. Here, we characterize, in detail, the development of neutralizing antibodies in three individuals coinfected with several divergent HIV variants. Two of these coinfected individuals developed additive or cross-neutralizing antibody responses. However, interference was observed in the third case, with neutralizing antibody responses to one viral variant arising to the near exclusion of neutralizing responses to the other. Longitudinal characterization of the diversity in the Envelope glycoprotein trimer (Env) structure showed that in the individual who developed the broadest neutralizing antibodies, circulating viruses shared a conserved epitope on the trimer apex that was targeted by cross-neutralizing antibodies. In contrast, in the other two individuals, diversity was distributed across Env. Taken together, these data highlight that multiple related immunogens can result in immune interference. However, they also suggest that immunogen cocktails presenting shared, conserved neutralizing epitopes in a variable background may focus broadly neutralizing antibody responses to these targets. IMPORTANCE Despite being the focus of extensive research, we still do not know how to reproducibly elicit cross-neutralizing antibodies against variable pathogens by vaccination. Here, we characterize the antibody responses in people coinfected with more than one HIV variant, providing insights into how the use of antigen "cocktails" might affect the breadth of the elicited neutralizing antibody response and how the relatedness of the antigens may shape this.
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Affiliation(s)
- Daniel J. Sheward
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tandile Hermanus
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Columbia University, New York, New York, USA
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Medical Research Council Antibody Immunity Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Medical Research Council Antibody Immunity Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Services of South Africa, Johannesburg, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Observatory, South Africa
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18
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Sheward DJ, Kim C, Ehling RA, Pankow A, Castro Dopico X, Dyrdak R, Martin DP, Reddy ST, Dillner J, Karlsson Hedestam GB, Albert J, Murrell B. Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. The Lancet Infectious Diseases 2022; 22:813-820. [PMID: 35305699 PMCID: PMC8930016 DOI: 10.1016/s1473-3099(22)00129-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022]
Abstract
Background The SARS-CoV-2 omicron (B.1.1.529) variant, which was first identified in November, 2021, spread rapidly in many countries, with a spike protein highly diverged from previously known variants, and raised concerns that this variant might evade neutralising antibody responses. We therefore aimed to characterise the sensitivity of the omicron variant to neutralisation. Methods For this cross-sectional study, we cloned the sequence encoding the omicron spike protein from a diagnostic sample to establish an omicron pseudotyped virus neutralisation assay. We quantified the neutralising antibody ID50 (the reciprocal dilution that produces 50% inhibition) against the omicron spike protein, and the fold-change in ID50 relative to the spike of wild-type SARS-CoV-2 (ie, the pandemic founder variant), for one convalescent reference plasma pool (WHO International Standard for anti-SARS-CoV-2 immunoglobulin [20/136]), three reference serum pools from vaccinated individuals, and two cohorts from Stockholm, Sweden: one comprising previously infected hospital workers (17 sampled in November, 2021, after vaccine rollout and nine in June or July, 2020, before vaccination) and one comprising serum from 40 randomly sampled blood donors donated during week 48 (Nov 29–Dec 5) of 2021. Furthermore, we assessed the neutralisation of omicron by five clinically relevant monoclonal antibodies (mAbs). Findings Neutralising antibody responses in reference sample pools sampled shortly after infection or vaccination were substantially less potent against the omicron variant than against wild-type SARS-CoV-2 (seven-fold to 42-fold reduction in ID50 titres). Similarly, for sera obtained before vaccination in 2020 from a cohort of convalescent hospital workers, neutralisation of the omicron variant was low to undetectable (all ID50 titres <20). However, in serum samples obtained in 2021 from two cohorts in Stockholm, substantial cross-neutralisation of the omicron variant was observed. Sera from 17 hospital workers after infection and subsequent vaccination had a reduction in average potency of only five-fold relative to wild-type SARS-CoV-2 (geometric mean ID50 titre 495 vs 105), and two donors had no reduction in potency. A similar pattern was observed in randomly sampled blood donors (n=40), who had an eight-fold reduction in average potency against the omicron variant compared with wild-type SARS-CoV-2 (geometric mean ID50 titre 369 vs 45). We found that the omicron variant was resistant to neutralisation (50% inhibitory concentration [IC50] >10 μg/mL) by mAbs casirivimab (REGN-10933), imdevimab (REGN-10987), etesevimab (Ly-CoV016), and bamlanivimab (Ly-CoV555), which form part of antibody combinations used in the clinic to treat COVID-19. However, S309, the parent of sotrovimab, retained most of its activity, with only an approximately two-fold reduction in potency against the omicron variant compared with ancestral D614G SARS-CoV-2 (IC50 0·1–0·2 μg/mL). Interpretation These data highlight the extensive, but incomplete, evasion of neutralising antibody responses by the omicron variant, and suggest that boosting with licensed vaccines might be sufficient to raise neutralising antibody titres to protective levels. Funding European Union Horizon 2020 research and innovation programme, European and Developing Countries Clinical Trials Partnership, SciLifeLab, and the Erling-Persson Foundation.
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19
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Hanke L, Sheward DJ, Pankow A, Vidakovics LP, Karl V, Kim C, Urgard E, Smith NL, Astorga-Wells J, Ekström S, Coquet JM, McInerney GM, Murrell B. Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies. Sci Adv 2022; 8:eabm0220. [PMID: 35333580 PMCID: PMC8956255 DOI: 10.1126/sciadv.abm0220] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 μg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L. Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Simon Ekström
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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20
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Castro Dopico X, Muschiol S, Grinberg NF, Aleman S, Sheward DJ, Hanke L, Ahl M, Vikström L, Forsell M, Coquet JM, McInerney G, Dillner J, Bogdanovic G, Murrell B, Albert J, Wallace C, Karlsson Hedestam GB. Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates. Clin Transl Immunology 2022; 11:e1379. [PMID: 35284072 PMCID: PMC8891432 DOI: 10.1002/cti2.1379] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 02/02/2023] Open
Abstract
Objectives Population-level measures of seropositivity are critical for understanding the epidemiology of an emerging pathogen, yet most antibody tests apply a strict cutoff for seropositivity that is not learnt in a data-driven manner, leading to uncertainty when classifying low-titer responses. To improve upon this, we evaluated cutoff-independent methods for their ability to assign likelihood of SARS-CoV-2 seropositivity to individual samples. Methods Using robust ELISAs based on SARS-CoV-2 spike (S) and the receptor-binding domain (RBD), we profiled antibody responses in a group of SARS-CoV-2 PCR+ individuals (n = 138). Using these data, we trained probabilistic learners to assign likelihood of seropositivity to test samples of unknown serostatus (n = 5100), identifying a support vector machines-linear discriminant analysis learner (SVM-LDA) suited for this purpose. Results In the training data from confirmed ancestral SARS-CoV-2 infections, 99% of participants had detectable anti-S and -RBD IgG in the circulation, with titers differing > 1000-fold between persons. In data of otherwise healthy individuals, 7.2% (n = 367) of samples were of uncertain serostatus, with values in the range of 3-6SD from the mean of pre-pandemic negative controls (n = 595). In contrast, SVM-LDA classified 6.4% (n = 328) of test samples as having a high likelihood (> 99% chance) of past infection, 4.5% (n = 230) to have a 50-99% likelihood, and 4.0% (n = 203) to have a 10-49% likelihood. As different probabilistic approaches were more consistent with each other than conventional SD-based methods, such tools allow for more statistically-sound seropositivity estimates in large cohorts. Conclusion Probabilistic antibody testing frameworks can improve seropositivity estimates in populations with large titer variability.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Sandra Muschiol
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden,Department of Clinical MicrobiologyKarolinska University HospitalStockholmSweden
| | - Nastasiya F Grinberg
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUK
| | - Soo Aleman
- Department of Infectious DiseasesKarolinska University HospitalHuddingeSweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Marcus Ahl
- Department of Infectious DiseasesKarolinska University HospitalHuddingeSweden
| | - Linnea Vikström
- Department of Clinical MicrobiologyUmeå UniversitetUmeåSweden
| | - Mattias Forsell
- Department of Clinical MicrobiologyUmeå UniversitetUmeåSweden
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Joakim Dillner
- Division of PathologyDepartment of Laboratory MedicineKarolinska InstitutetHuddingeSweden
| | - Gordana Bogdanovic
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden,Department of Clinical MicrobiologyKarolinska University HospitalStockholmSweden
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUK,Medical Research Council Biostatistics UnitUniversity of CambridgeCambridgeUK
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21
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Ehling RA, Weber CR, Mason DM, Friedensohn S, Wagner B, Bieberich F, Kapetanovic E, Vazquez-Lombardi R, Di Roberto RB, Hong KL, Wagner C, Pataia M, Overath MD, Sheward DJ, Murrell B, Yermanos A, Cuny AP, Savic M, Rudolf F, Reddy ST. SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display. Cell Rep 2022; 38:110242. [PMID: 34998467 PMCID: PMC8692065 DOI: 10.1016/j.celrep.2021.110242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023] Open
Abstract
Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).
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Affiliation(s)
- Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Raphaël B Di Roberto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland
| | | | - Michele Pataia
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Max D Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland; Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland; Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Andreas P Cuny
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland; Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland.
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22
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022; 13:155. [PMID: 35013189 PMCID: PMC8748511 DOI: 10.1038/s41467-021-27610-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [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: 04/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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23
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022. [PMID: 35013189 DOI: 10.1101/2021.03.20.436243v2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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24
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Sheward DJ, Mandolesi M, Urgard E, Kim C, Hanke L, Perez Vidakovics L, Pankow A, Smith NL, Castro Dopico X, McInerney GM, Coquet JM, Karlsson Hedestam GB, Murrell B. Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models. Cell Rep Med 2021; 2:100450. [PMID: 34723224 PMCID: PMC8536561 DOI: 10.1016/j.xcrm.2021.100450] [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: 05/11/2021] [Revised: 08/20/2021] [Accepted: 10/18/2021] [Indexed: 11/03/2022]
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) with resistance to neutralizing antibodies are threatening to undermine vaccine efficacy. Vaccination and infection have led to widespread humoral immunity against the pandemic founder (Wu-Hu-1). Against this background, it is critical to assess the outcomes of subsequent immunization with variant antigens. It is not yet clear whether heterotypic boosts would be compromised by original antigenic sin, where pre-existing responses to a prior variant dampen responses to a new one, or whether the memory B cell repertoire would bridge the gap between Wu-Hu-1 and VOCs. We show, in macaques immunized with Wu-Hu-1 spike, that a single dose of adjuvanted beta variant receptor binding domain (RBD) protein broadens neutralizing antibody responses to heterologous VOCs. Passive transfer of plasma sampled after Wu-Hu-1 spike immunization only partially protects K18-hACE2 mice from lethal challenge with a beta variant isolate, whereas plasma sampled following heterotypic RBD boost protects completely against disease.
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Affiliation(s)
- Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L. Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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25
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Mandolesi M, Sheward DJ, Hanke L, Ma J, Pushparaj P, Perez Vidakovics L, Kim C, Àdori M, Lenart K, Loré K, Castro Dopico X, Coquet JM, McInerney GM, Karlsson Hedestam GB, Murrell B. SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses. Cell Rep Med 2021; 2:100252. [PMID: 33842900 PMCID: PMC8020888 DOI: 10.1016/j.xcrm.2021.100252] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/05/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022]
Abstract
The outbreak and spread of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) is a current global health emergency, and effective prophylactic vaccines are needed urgently. The spike glycoprotein of SARS-CoV-2 mediates entry into host cells, and thus is the target of neutralizing antibodies. Here, we show that adjuvanted protein immunization with soluble SARS-CoV-2 spike trimers, stabilized in prefusion conformation, results in potent antibody responses in mice and rhesus macaques, with neutralizing antibody titers exceeding those typically measured in SARS-CoV-2 seropositive humans by more than one order of magnitude. Neutralizing antibody responses were observed after a single dose, with exceptionally high titers achieved after boosting. A follow-up to monitor the waning of the neutralizing antibody responses in rhesus macaques demonstrated durable responses that were maintained at high and stable levels at least 4 months after boosting. These data support the development of adjuvanted SARS-CoV-2 prefusion-stabilized spike protein subunit vaccines.
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Affiliation(s)
- Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Junjie Ma
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Klara Lenart
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Karin Loré
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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26
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Szurgot I, Hanke L, Sheward DJ, Vidakovics LP, Murrell B, McInerney GM, Liljeström P. DNA-launched RNA replicon vaccines induce potent anti-SARS-CoV-2 immune responses in mice. Sci Rep 2021; 11:3125. [PMID: 33542325 PMCID: PMC7862230 DOI: 10.1038/s41598-021-82498-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/07/2020] [Accepted: 01/20/2021] [Indexed: 12/23/2022] Open
Abstract
The outbreak of the SARS-CoV-2 virus and its rapid spread into a global pandemic made the urgent development of scalable vaccines to prevent coronavirus disease (COVID-19) a global health and economic imperative. Here, we characterized and compared the immunogenicity of two alphavirus-based DNA-launched self-replicating (DREP) vaccine candidates encoding either SARS-CoV-2 spike glycoprotein (DREP-S) or a spike ectodomain trimer stabilized in prefusion conformation (DREP-Secto). We observed that the two DREP constructs were immunogenic in mice inducing both binding and neutralizing antibodies as well as T cell responses. Interestingly, the DREP coding for the unmodified spike turned out to be more potent vaccine candidate, eliciting high titers of SARS-CoV-2 specific IgG antibodies that were able to efficiently neutralize pseudotyped virus after a single immunization. In addition, both DREP constructs were able to efficiently prime responses that could be boosted with a heterologous spike protein immunization. These data provide important novel insights into SARS-CoV-2 vaccine design using a rapid response DNA vaccine platform. Moreover, they encourage the use of mixed vaccine modalities as a strategy to combat SARS-CoV-2.
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Affiliation(s)
- Inga Szurgot
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Liljeström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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27
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Wørzner K, Sheward DJ, Schmidt ST, Hanke L, Zimmermann J, McInerney G, Karlsson Hedestam GB, Murrell B, Christensen D, Pedersen GK. Adjuvanted SARS-CoV-2 spike protein elicits neutralizing antibodies and CD4 T cell responses after a single immunization in mice. EBioMedicine 2021; 63:103197. [PMID: 33422991 PMCID: PMC7808923 DOI: 10.1016/j.ebiom.2020.103197] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/01/2020] [Accepted: 12/16/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SARS-CoV-2 has caused a global pandemic, infecting millions of people. A safe, effective vaccine is urgently needed and remains a global health priority. Subunit vaccines are used successfully against other viruses when administered in the presence of an effective adjuvant. METHODS We evaluated three different clinically tested adjuvant systems in combination with the SARS-CoV-2 pre-fusion stabilized (S-2P) spike protein using a one-dose regimen in mice. FINDINGS Whilst spike protein alone was only weakly immunogenic, the addition of either Aluminum hydroxide, a squalene based oil-in-water emulsion system (SE) or a cationic liposome-based adjuvant significantly enhanced antibody responses against the spike receptor binding domain (RBD). Kinetics of antibody responses differed, with SE providing the most rapid response. Neutralizing antibodies developed after a single immunization in all adjuvanted groups with ID50 titers ranging from 86-4063. Spike-specific CD4 T helper responses were also elicited, comprising mainly of IFN-γ and IL-17 producing cells in the cationic liposome adjuvanted group, and more IL-5- and IL-10-secreting cells in the AH group. INTERPRETATION These results demonstrate that adjuvanted spike protein subunit vaccine is a viable strategy for rapidly eliciting SARS-CoV-2 neutralizing antibodies and CD4 T cell responses of various qualities depending on the adjuvant used, which can be explored in further vaccine development against COVID-19. FUNDING This work was supported by the European Union Horizon 2020 research and innovation program under grant agreement no. 101003653.
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MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Immunologic/chemistry
- Aluminum Hydroxide/chemistry
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- CD4-Positive T-Lymphocytes/cytology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- COVID-19/pathology
- COVID-19/virology
- Female
- Immunization
- Interferon-gamma/metabolism
- Interleukin-17/metabolism
- Liposomes/chemistry
- Mice
- Mice, Inbred C57BL
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Squalene/chemistry
- Vaccines, Subunit/immunology
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Affiliation(s)
- Katharina Wørzner
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julie Zimmermann
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
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28
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Moliner-Morro A, J. Sheward D, Karl V, Perez Vidakovics L, Murrell B, McInerney GM, Hanke L. Picomolar SARS-CoV-2 Neutralization Using Multi-Arm PEG Nanobody Constructs. Biomolecules 2020; 10:biom10121661. [PMID: 33322557 PMCID: PMC7764822 DOI: 10.3390/biom10121661] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/29/2022] Open
Abstract
Multivalent antibody constructs have a broad range of clinical and biotechnological applications. Nanobodies are especially useful as components for multivalent constructs as they allow increased valency while maintaining a small molecule size. We here describe a novel, rapid method for the generation of bi- and multivalent nanobody constructs with oriented assembly by Cu-free strain promoted azide-alkyne click chemistry (SPAAC). We used sortase A for ligation of click chemistry functional groups site-specifically to the C-terminus of nanobodies before creating C-to-C-terminal nanobody fusions and 4-arm polyethylene glycol (PEG) tetrameric nanobody constructs. We demonstrated the viability of this approach by generating constructs with the SARS-CoV-2 neutralizing nanobody Ty1. We compared the ability of the different constructs to neutralize SARS-CoV-2 pseudotyped virus and infectious virus in neutralization assays. The generated dimers neutralized the virus similarly to a nanobody-Fc fusion variant, while a 4-arm PEG based tetrameric Ty1 construct dramatically enhanced neutralization of SARS-CoV-2, with an IC50 in the low picomolar range.
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Affiliation(s)
- Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
- Correspondence:
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29
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Custódio TF, Das H, Sheward DJ, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer MA, Gruzinov AY, Jeffries CM, Graewert MA, Svergun DI, Dobrev N, Remans K, Seeger MA, McInerney GM, Murrell B, Hällberg BM, Löw C. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2. Nat Commun 2020; 11:5588. [PMID: 33149112 PMCID: PMC7642358 DOI: 10.1038/s41467-020-19204-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [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: 06/16/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50 of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed an unusual conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.
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Affiliation(s)
- Tânia F Custódio
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Hrishikesh Das
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Samuel Pazicky
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Joanna Pieprzyk
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Martin A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Andrey Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Melissa A Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Nikolay Dobrev
- European Molecular Biology Laboratory (EMBL) Heidelberg, Protein Expression and Purification Core Facility, 69117, Heidelberg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL) Heidelberg, Protein Expression and Purification Core Facility, 69117, Heidelberg, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
| | - B Martin Hällberg
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, D-22607, Hamburg, Germany.
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177, Stockholm, Sweden.
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.
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30
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Hanke L, Vidakovics Perez L, Sheward DJ, Das H, Schulte T, Moliner-Morro A, Corcoran M, Achour A, Karlsson Hedestam GB, Hällberg BM, Murrell B, McInerney GM. An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun 2020; 11:4420. [PMID: 32887876 DOI: 10.1101/2020.06.02.130161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/08/2020] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Angiotensin-Converting Enzyme Inhibitors/pharmacology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Camelids, New World/immunology
- Chlorocebus aethiops
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cryoelectron Microscopy
- Epitopes/immunology
- Epitopes/metabolism
- HEK293 Cells
- Humans
- Male
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Vidakovics Perez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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31
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Hanke L, Vidakovics Perez L, Sheward DJ, Das H, Schulte T, Moliner-Morro A, Corcoran M, Achour A, Karlsson Hedestam GB, Hällberg BM, Murrell B, McInerney GM. An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun 2020; 11:4420. [PMID: 32887876 PMCID: PMC7473855 DOI: 10.1038/s41467-020-18174-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022] Open
Abstract
SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Angiotensin-Converting Enzyme Inhibitors/pharmacology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Camelids, New World/immunology
- Chlorocebus aethiops
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cryoelectron Microscopy
- Epitopes/immunology
- Epitopes/metabolism
- HEK293 Cells
- Humans
- Male
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Vidakovics Perez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Sheward DJ, Marais J, Bekker V, Murrell B, Eren K, Bhiman JN, Nonyane M, Garrett N, Woodman ZL, Abdool Karim Q, Abdool Karim SS, Morris L, Moore PL, Williamson C. HIV Superinfection Drives De Novo Antibody Responses and Not Neutralization Breadth. Cell Host Microbe 2018; 24:593-599.e3. [PMID: 30269971 PMCID: PMC6185870 DOI: 10.1016/j.chom.2018.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/07/2018] [Revised: 07/10/2018] [Accepted: 09/04/2018] [Indexed: 02/08/2023]
Abstract
Eliciting antibodies that neutralize a broad range of circulating HIV strains (broadly neutralizing antibodies [bnAbs]) represents a key priority for vaccine development. HIV superinfection (re-infection with a second strain following an established infection) has been associated with neutralization breadth, and can provide insights into how the immune system responds to sequential exposure to distinct HIV envelope glycoproteins (Env). Characterizing the neutralizing antibody (nAb) responses in four superinfected women revealed that superinfection does not boost memory nAb responses primed by the first infection or promote nAb responses to epitopes conserved in both infecting viruses. While one superinfected individual developed potent bnAbs, superinfection was likely not the driver as the nAb response did not target an epitope conserved in both viruses. Rather, sequential exposure led to nAbs specific to each Env but did not promote bnAb development. Thus, sequential immunization with heterologous Envs may not be sufficient to focus the immune response onto conserved epitopes. HIV superinfection does not efficiently recruit cross-reactive memory B cells Superinfection results in antibody responses specific to each infecting strain No evidence that superinfection drives the development of bnAbs
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Affiliation(s)
- Daniel J Sheward
- Division of Medical Virology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Jinny Marais
- Division of Medical Virology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Valerie Bekker
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Kemal Eren
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA 92093, USA
| | - Jinal N Bhiman
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa; University of Witwatersrand, Johannesburg 2050, South Africa
| | - Molati Nonyane
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa
| | - Zenda L Woodman
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7700, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa; Department of Epidemiology, Columbia University, New York, NY 10027, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa; Department of Epidemiology, Columbia University, New York, NY 10027, USA
| | - Lynn Morris
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa; University of Witwatersrand, Johannesburg 2050, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa
| | - Penny L Moore
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg 2192, South Africa; University of Witwatersrand, Johannesburg 2050, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa.
| | - Carolyn Williamson
- Division of Medical Virology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa; National Health Laboratory Services of South Africa, Cape Town 7925, South Africa.
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33
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Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Karim SA, Karim QA, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Correction: Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog 2017; 13:e1006641. [PMID: 28945784 PMCID: PMC5612725 DOI: 10.1371/journal.ppat.1006641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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34
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Wibmer CK, Gorman J, Ozorowski G, Bhiman JN, Sheward DJ, Elliott DH, Rouelle J, Smira A, Joyce MG, Ndabambi N, Druz A, Asokan M, Burton DR, Connors M, Abdool Karim SS, Mascola JR, Robinson JE, Ward AB, Williamson C, Kwong PD, Morris L, Moore PL. Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface Antibody that Caused MPER Exposure through Viral Escape. PLoS Pathog 2017; 13:e1006074. [PMID: 28076415 PMCID: PMC5226681 DOI: 10.1371/journal.ppat.1006074] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
A comprehensive understanding of the regions on HIV-1 envelope trimers targeted by broadly neutralizing antibodies may contribute to rational design of an HIV-1 vaccine. We previously identified a participant in the CAPRISA cohort, CAP248, who developed trimer-specific antibodies capable of neutralizing 60% of heterologous viruses at three years post-infection. Here, we report the isolation by B cell culture of monoclonal antibody CAP248-2B, which targets a novel membrane proximal epitope including elements of gp120 and gp41. Despite low maximum inhibition plateaus, often below 50% inhibitory concentrations, the breadth of CAP248-2B significantly correlated with donor plasma. Site-directed mutagenesis, X-ray crystallography, and negative-stain electron microscopy 3D reconstructions revealed how CAP248-2B recognizes a cleavage-dependent epitope that includes the gp120 C terminus. While this epitope is distinct, it overlapped in parts of gp41 with the epitopes of broadly neutralizing antibodies PGT151, VRC34, 35O22, 3BC315, and 10E8. CAP248-2B has a conformationally variable paratope with an unusually long 19 amino acid light chain third complementarity determining region. Two phenylalanines at the loop apex were predicted by docking and mutagenesis data to interact with the viral membrane. Neutralization by CAP248-2B is not dependent on any single glycan proximal to its epitope, and low neutralization plateaus could not be completely explained by N- or O-linked glycosylation pathway inhibitors, furin co-transfection, or pre-incubation with soluble CD4. Viral escape from CAP248-2B involved a cluster of rare mutations in the gp120-gp41 cleavage sites. Simultaneous introduction of these mutations into heterologous viruses abrogated neutralization by CAP248-2B, but enhanced neutralization sensitivity to 35O22, 4E10, and 10E8 by 10-100-fold. Altogether, this study expands the region of the HIV-1 gp120-gp41 quaternary interface that is a target for broadly neutralizing antibodies and identifies a set of mutations in the gp120 C terminus that exposes the membrane-proximal external region of gp41, with potential utility in HIV vaccine design.
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Affiliation(s)
- Constantinos Kurt Wibmer
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Jinal N. Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel J. Sheward
- Institute of Infectious Disease and Molecular Medicine (IDM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
| | - Debra H. Elliott
- Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Julie Rouelle
- Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Ashley Smira
- Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - M. Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nonkululeko Ndabambi
- Institute of Infectious Disease and Molecular Medicine (IDM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mangai Asokan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbial Science, CHAVI-ID and IAVI Neutralizing Antibody Centre, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Columbia University, New York, New York, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James E. Robinson
- Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine (IDM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- 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, Durban, South Africa
| | - Penny L. Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- 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, Durban, South Africa
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35
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Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog 2016; 12:e1005742. [PMID: 27434311 PMCID: PMC4951126 DOI: 10.1371/journal.ppat.1005742] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 06/09/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
The development of biomedical interventions to reduce acquisition of HIV-1 infection remains a global priority, however their potential effectiveness is challenged by very high HIV-1 envelope diversity. Two large prophylactic trials in high incidence, clade C epidemic regions in southern Africa are imminent; passive administration of the monoclonal antibody VRC01, and active immunization with a clade C modified RV144-like vaccines. We have created a large representative panel of C clade viruses to enable assessment of antibody responses to vaccines and natural infection in Southern Africa, and we investigated the genotypic and neutralization properties of recently transmitted clade C viruses to determine how viral diversity impacted antibody recognition. We further explore the implications of these findings for the potential effectiveness of these trials. A panel of 200 HIV-1 Envelope pseudoviruses was constructed from clade C viruses collected within the first 100 days following infection. Viruses collected pre-seroconversion were significantly more resistant to serum neutralization compared to post-seroconversion viruses (p = 0.001). Over 13 years of the study as the epidemic matured, HIV-1 diversified (p = 0.0009) and became more neutralization resistant to monoclonal antibodies VRC01, PG9 and 4E10. When tested at therapeutic levels (10ug/ml), VRC01 only neutralized 80% of viruses in the panel, although it did exhibit potent neutralization activity against sensitive viruses (IC50 titres of 0.42 μg/ml). The Gp120 amino acid similarity between the clade C panel and candidate C-clade vaccine protein boosts (Ce1086 and TV1) was 77%, which is 8% more distant than between CRF01_AE viruses and the RV144 CRF01_AE immunogen. Furthermore, two vaccine signature sites, K169 in V2 and I307 in V3, associated with reduced infection risk in RV144, occurred less frequently in clade C panel viruses than in CRF01_AE viruses from Thailand. Increased resistance of pre-seroconversion viruses and evidence of antigenic drift highlights the value of using panels of very recently transmitted viruses and suggests that interventions may need to be modified over time to track the changing epidemic. Furthermore, high divergence such as that observed in the older clade C epidemic in southern Africa may impact vaccine efficacy, although the correlates of infection risk are yet to be defined in the clade C setting. Findings from this study of acute/early clade C viruses will aid vaccine development, and enable identification of new broad and potent antibodies to combat the HIV-1 C-clade epidemic in southern Africa.
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Affiliation(s)
- Cecilia Rademeyer
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Bette Korber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Elena E. Giorgi
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Ruwayhida Thebus
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Alexander Robles
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Daniel J. Sheward
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Kshitij Wagh
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Jetta Garrity
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Brittany R. Carey
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli M. Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Gama P. Bandawe
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Jinny C. Marais
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | | | - Peter Hraber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Nancy Tumba
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Glenda E. Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and South African Medical Research Council, Cape Town, South Africa
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marion Vermeulen
- South African National Blood Service, Weltevreden Park, South Africa
| | - Keren Middelkoop
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Michael Hoelscher
- Department for Infectious Diseases & Tropical Medicine, Klinikum University of Munich, LMU and German Center for Infection Research (DZIF) partner site Munich, Munich, Germany
| | | | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- International Vaccine Institute, Seoul, Republic of Korea
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Feng Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lynn Morris
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carolyn Williamson
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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36
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Richardson SI, Gray ES, Mkhize NN, Sheward DJ, Lambson BE, Wibmer CK, Masson L, Werner L, Garrett N, Passmore JAS, Karim QA, Karim SSA, Williamson C, Moore PL, Morris L. South African HIV-1 subtype C transmitted variants with a specific V2 motif show higher dependence on α4β7 for replication. Retrovirology 2015; 12:54. [PMID: 26105197 PMCID: PMC4479312 DOI: 10.1186/s12977-015-0183-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 03/06/2015] [Accepted: 06/15/2015] [Indexed: 12/03/2022] Open
Abstract
Background The integrin α4β7 mediates the trafficking of immune cells to the gut associated lymphoid tissue (GALT) and is an attachment factor for the HIV gp120 envelope glycoprotein. We developed a viral replication inhibition assay to more clearly evaluate the role of α4β7 in HIV infection and the contribution of viral and host factors. Results Replication of 60 HIV-1 subtype C viruses collected over time from 11 individuals in the CAPRISA cohort were partially inhibited by antibodies targeting α4β7. However, dependence on α4β7 for replication varied substantially among viral isolates from different individuals as well as over time in some individuals. Among 8 transmitted/founder (T/F) viruses, α4β7 reactivity was highest for viruses having P/SDI/V tri-peptide binding motifs. Mutation of T/F viruses that had LDI/L motifs to P/SDI/V resulted in greater α4β7 reactivity, whereas mutating P/SDI/V to LDI/L motifs was associated with reduced α4β7 binding. P/SDI/V motifs were more common among South African HIV subtype C viruses (35%) compared to subtype C viruses from other regions of Africa (<8%) and to other subtypes, due in part to a founder effect. In addition, individuals with bacterial vaginosis (BV) and who had higher concentrations of IL-7, IL-8 and IL-1α in the genital tract had T/F viruses with higher α4β7 dependence for replication, suggesting that viruses with P/SDI/V motifs may be preferentially transmitted in the presence of BV in this population. Conclusions Collectively, these data suggest a role for α4β7 in HIV infection that is influenced by both viral and host factors including the sequence of the α4β7 binding motif, the cytokine milieu and BV in the genital tract. The higher frequency of P/SDI/V sequences among South African HIV-1 subtype C viruses may have particular significance for the role of α4β7 in this geographical region. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0183-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simone I Richardson
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Elin S Gray
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,ECU Melanoma Research Foundation, Edith Cowan University (ECU), Perth, WA, 6027, Australia.
| | - Nonhlanhla N Mkhize
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Daniel J Sheward
- Divison of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
| | - Bronwen E Lambson
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Constantinos Kurt Wibmer
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Lindi Masson
- Divison of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
| | - Lise Werner
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Jo-Ann S Passmore
- Divison of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. .,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,National Health Laboratory Service, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,Department of Epidemiology, Columbia University, New York, NY, USA.
| | - Carolyn Williamson
- Divison of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. .,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa. .,National Health Laboratory Service, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Penny L Moore
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,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, Durban, South Africa.
| | - Lynn Morris
- Centre for HIV and STI's, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,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, Durban, South Africa.
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37
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Sheward DJ, Ntale R, Garrett NJ, Woodman ZL, Abdool Karim SS, Williamson C. HIV-1 Superinfection Resembles Primary Infection. J Infect Dis 2015; 212:904-8. [PMID: 25754982 DOI: 10.1093/infdis/jiv136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/23/2015] [Indexed: 11/12/2022] Open
Abstract
The relevance of superinfection as a model to identify correlates of protection against human immunodeficiency virus (HIV) depends on whether the superinfecting transmission resembles primary infection, which has not been established. Here, we characterize the genetic bottleneck in superinfected individuals for the first time. In all 3 cases, superinfection produced a spike in viral load and could be traced to a single, C-C chemokine receptor 5-tropic founder virus with shorter, less glycosylated variable regions than matched chronic viruses. These features are consistent with primary HIV transmission and provide support for the use of superinfection as a model to address correlates of protection against HIV.
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Affiliation(s)
- Daniel J Sheward
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa
| | - Roman Ntale
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa Department of Biomedical Laboratory Sciences, College of Medicine and Health Sciences, Kigali, Rwanda
| | - Nigel J Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA) Department of Infectious Diseases, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban
| | - Zenda L Woodman
- Department of Molecular and Cell Biology, University of Cape Town
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA) Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Carolyn Williamson
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa Centre for the AIDS Programme of Research in South Africa (CAPRISA) National Health Laboratory Services, Johannesburg, South Africa
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38
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Bandawe GP, Moore PL, Werner L, Gray ES, Sheward DJ, Madiga M, Nofemela A, Thebus R, Marais JC, Maboko L, Abdool Karim SS, Hoelscher M, Morris L, Williamson C. Differences in HIV type 1 neutralization breadth in 2 geographically distinct cohorts in Africa. J Infect Dis 2014; 211:1461-6. [PMID: 25398460 DOI: 10.1093/infdis/jiu633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 10/28/2014] [Indexed: 11/14/2022] Open
Abstract
To investigate whether distinct populations have differing human immunodeficiency virus type 1 (HIV) neutralizing antibody responses, we compared 20 women from Tanzania's HIV Superinfection Study (HISIS) cohort, who were infected multiple HIV subtypes, and 22 women from the Centre for the AIDS Programme of Research in South Africa (CAPRISA) cohort, who were infected exclusively with HIV subtype C. By 2 years after infection, 35% of HISIS subjects developed neutralization breadth, compared with 9% of CAPRISA subjects (P = .0131). Cumulative viral loads between 3 and 12 months were higher in the HISIS group (P = .046) and strongly associated with breadth (P < .0001). While viral load was the strongest predictor, other factors may play a role, as the odds of developing breadth remained higher in HISIS even after correction for viral load.
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Affiliation(s)
- Gama P Bandawe
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services School of Pathology, University of the Witwatersrand, Johannesburg Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Lise Werner
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Elin S Gray
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services
| | - Daniel J Sheward
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town
| | - Maphuti Madiga
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services
| | - Andile Nofemela
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town
| | - Ruwayhida Thebus
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town
| | - Jinny C Marais
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town
| | | | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, Klinikum of Ludwig Maximilians University German Center for Infection Research, Partner Site Munich, Germany
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services School of Pathology, University of the Witwatersrand, Johannesburg Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine Division of Medical Virology, University of Cape Town National Health Laboratory Services, Cape Town Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
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39
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Bhiman JN, Doria-Rose NA, Wibmer CK, Sheward DJ, Williamson C, Karim SSA, Kwong PD, Mascola JR, Morris L, Moore PL. Maturation of Broadly Neutralizing V1V2-directed Antibodies in the Context of Autologous Viral Escape. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5053.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jinal N. Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, South Africa
| | - Constantinos Kurt Wibmer
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel J. Sheward
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, South Africa
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, 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, Durban, South Africa
| | - Penny L. Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, 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, Durban, South Africa
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40
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Logan MG, Sheward DJ, Anthony C, Garret N, Williamson C. Changes in Viral Population Kinetics Following HIV-1 Superinfection. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5493.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Murray G. Logan
- University of Cape Town, Clinical Laboratory Sciences, Cape Town, South Africa
| | - Daniel J. Sheward
- University of Cape Town, Clinical Laboratory Sciences, Cape Town, South Africa
| | - Colin Anthony
- University of Cape Town, Clinical Laboratory Sciences, Cape Town, South Africa
| | - Nigel Garret
- CAPRISA/University of Kwa Zulu Natal, Durban, South Africa
| | - Carolyn Williamson
- University of Cape Town, Clinical Laboratory Sciences, Cape Town, South Africa
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41
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Wibmer CK, Sheward DJ, Bhiman JN, Ndabambi N, Elliot DH, Rouelle J, Smira A, Karim SSA, Robinson JE, Morris L, Williamson C, Moore PL. Viral Escape Pathways from Broadly Neutralising Antibodies Targeting the HIV Envelope Cleavage Site Enhance MPER Mediated Neutralisation. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5026.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Constantinos Kurt Wibmer
- Centre for HIV & STIs, National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel J. Sheward
- Institute of Infectious Disease and Molecular Medicine (IIDMM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
| | - Jinal N. Bhiman
- Centre for HIV & STIs, National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonkululeko Ndabambi
- Institute of Infectious Disease and Molecular Medicine (IIDMM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
| | - Debra H. Elliot
- Tulane University Medical Center, Department of Pediatrics, New Orleans, LA, United States
| | - Julie Rouelle
- Tulane University Medical Center, Department of Pediatrics, New Orleans, LA, United States
| | - Ashley Smira
- Tulane University Medical Center, Department of Pediatrics, New Orleans, LA, United States
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. Robinson
- Tulane University Medical Center, Department of Pediatrics, New Orleans, LA, United States
| | - Lynn Morris
- Centre for HIV & STIs, National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine (IIDMM) and Division of Medical Virology, University of Cape Town and NHLS, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Penny L. Moore
- Centre for HIV & STIs, National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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42
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Moore PL, Gray ES, Wibmer CK, Bhiman JN, Nonyane M, Sheward DJ, Hermanus T, Bajimaya S, Tumba NL, Abrahams MR, Lambson BE, Ranchobe N, Ping L, Ngandu N, Abdool Karim Q, Abdool Karim SS, Swanstrom RI, Seaman MS, Williamson C, Morris L. Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape. Nat Med 2012; 18:1688-92. [PMID: 23086475 DOI: 10.1038/nm.2985] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/27/2012] [Indexed: 12/27/2022]
Abstract
Neutralizing antibodies are likely to play a crucial part in a preventative HIV-1 vaccine. Although efforts to elicit broadly cross-neutralizing (BCN) antibodies by vaccination have been unsuccessful, a minority of individuals naturally develop these antibodies after many years of infection. How such antibodies arise, and the role of viral evolution in shaping these responses, is unknown. Here we show, in two HIV-1-infected individuals who developed BCN antibodies targeting the glycan at Asn332 on the gp120 envelope, that this glycan was absent on the initial infecting virus. However, this BCN epitope evolved within 6 months, through immune escape from earlier strain-specific antibodies that resulted in a shift of a glycan to position 332. Both viruses that lacked the glycan at amino acid 332 were resistant to the Asn332-dependent BCN monoclonal antibody PGT128 (ref. 8), whereas escaped variants that acquired this glycan were sensitive. Analysis of large sequence and neutralization data sets showed the 332 glycan to be significantly under-represented in transmitted subtype C viruses compared to chronic viruses, with the absence of this glycan corresponding with resistance to PGT128. These findings highlight the dynamic interplay between early antibodies and viral escape in driving the evolution of conserved BCN antibody epitopes.
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Affiliation(s)
- Penny L Moore
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
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