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      An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

      research-article
      1 , 1 , 2 , 1 , 3 , 4 , 3 , 4 , 1 , 1 , 5 , 6 , 1 , 3 , 4 , 1 , 3 , 4 , 7 , 7 , 5 , 6 , 5 , 6 , 5 , 6 , 5 , 6 , 5 , 6 , 8 , 1 , 9 , 10 , 11 , 1 , 12 , 9 , 10 , 1 , 12 , 6 , 7 , 4 , 13 , 1 , 1 , ^ , , 1 , 3 , 4 , ^ , , 1 , 2 , 12 , ^ ,
      Science Translational Medicine
      American Association for the Advancement of Science

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          Abstract

          The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well-conserved among sarbecoviruses, but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.

          Abstract

          A monoclonal antibody that neutralizes or binds all sarbecoviruses tested is representative of a reproducible antibody class.

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          Most cited references62

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Visualization
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing - original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: Formal analysisRole: InvestigationRole: Resources
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: InvestigationRole: Validation
                Role: MethodologyRole: Resources
                Role: Investigation
                Role: Investigation
                Role: InvestigationRole: MethodologyRole: Resources
                Role: Investigation
                Role: InvestigationRole: Resources
                Role: InvestigationRole: Resources
                Role: InvestigationRole: MethodologyRole: ResourcesRole: Validation
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: Project administrationRole: Resources
                Role: Funding acquisitionRole: MethodologyRole: ResourcesRole: Supervision
                Role: Resources
                Role: ConceptualizationRole: ResourcesRole: Validation
                Role: InvestigationRole: MethodologyRole: Resources
                Role: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: Writing - review & editing
                Role: ConceptualizationRole: Project administrationRole: ResourcesRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: Project administrationRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: VisualizationRole: Writing - original draft
                Journal
                Sci Transl Med
                Sci Transl Med
                stm
                Science Translational Medicine
                American Association for the Advancement of Science
                1946-6234
                1946-6242
                19 April 2022
                19 April 2022
                : eabn6859
                Affiliations
                [ 1 ]Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
                [ 2 ]Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
                [ 3 ]Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
                [ 4 ]Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
                [ 5 ]State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
                [ 6 ]Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
                [ 7 ]Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
                [ 8 ]AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
                [ 9 ]Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
                [ 10 ]Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
                [ 11 ]Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
                [ 12 ]Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
                [ 13 ]Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
                Author notes
                [* ]

                These authors contributed equally

                [ ^ ]Address correspondence to David D. Ho ( dh2994@ 123456cumc.columbia.edu , 212-304-6101, 701 W 168 th St, 11 th Floor, New York, NY 10032), Lawrence Shapiro ( lss8@ 123456columbia.edu ), or Yaoxing Huang ( yh3253@ 123456cumc.columbia.edu )
                Author information
                https://orcid.org/0000-0003-3128-8513
                https://orcid.org/0000-0002-3733-9556
                https://orcid.org/0000-0001-5357-660X
                https://orcid.org/0000-0002-2910-0908
                https://orcid.org/0000-0003-3054-5506
                https://orcid.org/0000-0002-5994-3957
                https://orcid.org/0000-0001-8604-4538
                https://orcid.org/0000-0001-6336-6657
                https://orcid.org/0000-0002-9081-7561
                https://orcid.org/0000-0002-8129-4033
                https://orcid.org/0000-0003-2410-9361
                https://orcid.org/0000-0001-6858-5306
                https://orcid.org/0000-0003-2855-9837
                https://orcid.org/0000-0001-7996-1119
                https://orcid.org/0000-0002-7737-8912
                https://orcid.org/0000-0001-7089-4829
                https://orcid.org/0000-0002-4511-2888
                https://orcid.org/0000-0003-3277-8792
                https://orcid.org/0000-0003-3064-8265
                https://orcid.org/0000-0002-9346-9056
                https://orcid.org/0000-0002-1268-5524
                https://orcid.org/0000-0001-8587-277X
                https://orcid.org/0000-0001-8700-4570
                https://orcid.org/0000-0003-3560-232X
                https://orcid.org/0000-0002-3253-3309
                https://orcid.org/0000-0001-6270-1644
                https://orcid.org/0000-0001-9943-8819
                https://orcid.org/0000-0003-1627-149X
                Article
                abn6859
                10.1126/scitranslmed.abn6859
                9017343
                35438546
                433fac1f-b052-4319-a5ad-ae99e0daa06e
                Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 December 2021
                : 07 April 2022
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000865, Bill and Melinda Gates Foundation;
                Funded by: FundRef http://dx.doi.org/10.13039/100006474, Columbia University;
                Funded by: FundRef http://dx.doi.org/10.13039/100007457, JPB Foundation;
                Funded by: FundRef , Andrews and Peggy Cherng;
                Funded by: FundRef , Samuel Yin;
                Funded by: FundRef , Carol Ludwig;
                Funded by: FundRef , David and Roger Wu;
                Funded by: FundRef , Health@InnoHK;
                Categories
                Research Article
                Research Articles
                STM r-articles
                Coronavirus
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