Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain

[1]  D. Stuart,et al.  Antibody evasion by the P.1 strain of SARS-CoV-2 , 2021, Cell.

[2]  Ahmed Abdul Azim,et al.  Immunogenicity of the Ad26.COV2.S Vaccine for COVID-19. , 2021, JAMA.

[3]  A. Godzik,et al.  Detection of a SARS-CoV-2 variant of concern in South Africa , 2021, Nature.

[4]  L. Morris,et al.  SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma , 2021, Nature Medicine.

[5]  D. Stuart,et al.  Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera , 2021, Cell.

[6]  D. Burton,et al.  Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants , 2021, Science.

[7]  M. Nussenzweig,et al.  mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants , 2021, Nature.

[8]  M. Nussenzweig,et al.  mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants , 2021, bioRxiv.

[9]  L. Morris,et al.  SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma , 2021, bioRxiv.

[10]  M. Nussenzweig,et al.  Evolution of antibody immunity to SARS-CoV-2 , 2021, Nature.

[11]  H. Schuitemaker,et al.  Interim Results of a Phase 1–2a Trial of Ad26.COV2.S Covid-19 Vaccine , 2021, The New England journal of medicine.

[12]  J. Bloom,et al.  Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies , 2021, bioRxiv.

[13]  Rommie E. Amaro,et al.  SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma , 2020, bioRxiv.

[14]  A. Tanuri,et al.  Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil , 2020, Journal of Virology.

[15]  Paul J. Steiner,et al.  Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses , 2020, bioRxiv.

[16]  S. Dübel,et al.  A SARS-CoV-2 Neutralizing Antibody Selected from COVID-19 Patients by Phage Display is Binding to the ACE2-RBD Interface and is Tolerant to Known RBD Mutations , 2020, SSRN Electronic Journal.

[17]  Ping Li,et al.  Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine , 2020 .

[18]  Marcio K. Oikawa,et al.  Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic , 2020, Science.

[19]  Nguyen H. Tran,et al.  Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK , 2020, Lancet.

[20]  Elisabeth Mahase Covid-19: Moderna applies for US and EU approval as vaccine trial reports 94.1% efficacy , 2020, BMJ.

[21]  Nguyen H. Tran,et al.  Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial. , 2020, Lancet.

[22]  Elisabeth Mahase Covid-19: Moderna vaccine is nearly 95% effective, trial involving high risk and elderly people shows , 2020, BMJ.

[23]  A. Griffiths,et al.  Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2 , 2020, bioRxiv.

[24]  M. Nussenzweig,et al.  Evolution of Antibody Immunity to SARS-CoV-2 , 2020, bioRxiv.

[25]  D. Qu,et al.  A Rapid and Efficient Screening System for Neutralizing Antibodies and Its Application for SARS-CoV-2 , 2020, Frontiers in Immunology.

[26]  C. Cordon-Cardo,et al.  Robust neutralizing antibodies to SARS-CoV-2 infection persist for months , 2020, Science.

[27]  L. Stamatatos,et al.  Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation , 2020, Nature Communications.

[28]  C. Rice,et al.  Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants , 2020, bioRxiv.

[29]  L. Forni,et al.  COVID-19-associated acute kidney injury: consensus report of the 25th Acute Disease Quality Initiative (ADQI) Workgroup , 2020, Nature Reviews Nephrology.

[30]  M. Nussenzweig,et al.  SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies , 2020, Nature.

[31]  I. Wilson,et al.  Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies , 2020, Biochemical and Biophysical Research Communications.

[32]  I. Wilson,et al.  An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain , 2020, Cell Reports.

[33]  F. Krammer SARS-CoV-2 vaccines in development , 2020, Nature.

[34]  M. Endres,et al.  A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model , 2020, Cell.

[35]  Peter B Rosenthal,et al.  Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion , 2020, Nature.

[36]  X. Xie,et al.  Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy , 2020, Cell.

[37]  Sarah K. Hilton,et al.  Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition , 2020, bioRxiv.

[38]  Howard Y. Chang,et al.  Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2 , 2020, Cell Host & Microbe.

[39]  J. Sodroski,et al.  Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike , 2020, Nature.

[40]  C. Rice,et al.  Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants , 2020, bioRxiv.

[41]  Nguyen H. Tran,et al.  Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial , 2020, The Lancet.

[42]  Xuguang Li,et al.  The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity , 2020, Cell.

[43]  D. Burton,et al.  Structural basis of a shared antibody response to SARS-CoV-2 , 2020, Science.

[44]  Samuel B. Day,et al.  Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein , 2020, Nature Medicine.

[45]  Howard Y. Chang,et al.  Human B cell clonal expansion and convergent antibody responses to SARS CoV-2 , 2020, bioRxiv.

[46]  M. Nussenzweig,et al.  Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies , 2020, Cell.

[47]  Qiang Zhou,et al.  A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 , 2020, Science.

[48]  D. Burton,et al.  Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model , 2020, Science.

[49]  C. Rice,et al.  Convergent Antibody Responses to SARS-CoV-2 in Convalescent Individuals , 2020, Nature.

[50]  L. Gieselmann,et al.  Longitudinal Isolation of Potent Near-Germline SARS-CoV-2-Neutralizing Antibodies from COVID-19 Patients , 2020, Cell.

[51]  L. Stamatatos,et al.  Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation , 2020, bioRxiv.

[52]  A. Sette,et al.  The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients , 2020, Science Immunology.

[53]  L. Stamatatos,et al.  Analysis of a SARS-CoV-2-Infected Individual Reveals Development of Potent Neutralizing Antibodies with Limited Somatic Mutation , 2020, Immunity.

[54]  M. Nussenzweig,et al.  Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies , 2020, bioRxiv.

[55]  William J. Liu,et al.  A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2 , 2020, Nature.

[56]  Linqi Zhang,et al.  Human neutralizing antibodies elicited by SARS-CoV-2 infection , 2020, Nature.

[57]  H. Achdout,et al.  Tiger team: a panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes , 2020, bioRxiv.

[58]  Xiangxi Wang,et al.  Human-IgG-Neutralizing Monoclonal Antibodies Block the SARS-CoV-2 Infection , 2020, bioRxiv.

[59]  X. Xie,et al.  Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells , 2020, Cell.

[60]  Amalio Telenti,et al.  Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody , 2020, Nature.

[61]  Samuel B. Day,et al.  Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein , 2020, bioRxiv.

[62]  M. V. van Breemen,et al.  Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability , 2020, Science.

[63]  F. Gao,et al.  A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2 , 2020, Science.

[64]  C. Hillyer,et al.  Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses , 2020, Trends in Immunology.

[65]  F. Krammer,et al.  SARS-CoV-2 Vaccines: Status Report , 2020, Immunity.

[66]  Nicholas C. Wu,et al.  A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV , 2020, Science.

[67]  K. Yuen,et al.  Clinical Characteristics of Coronavirus Disease 2019 in China , 2020, The New England journal of medicine.

[68]  M. Letko,et al.  Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses , 2020, Nature Microbiology.

[69]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[70]  Ralph S. Baric,et al.  Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus , 2020, Journal of Virology.

[71]  G. Gao,et al.  A Novel Coronavirus from Patients with Pneumonia in China, 2019 , 2020, The New England journal of medicine.

[72]  Mikael Olsson Struct , 2019, C# 8 Quick Syntax Reference.

[73]  Dimitri Schritt,et al.  Modeling of stimuli-responsive nanoreactors: rational rate control towards the design of colloidal enzymes , 2019, Molecular Systems Design & Engineering.

[74]  C. Deane,et al.  Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires , 2018, The Journal of Immunology.

[75]  Lynn Morris,et al.  Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection , 2018, Cell host & microbe.

[76]  Peter D. Crompton,et al.  Public antibodies to malaria antigens generated by two LAIR1 insertion modalities , 2017, Nature.

[77]  R. Lerner,et al.  In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity , 2017, Nature Communications.

[78]  P. Wilson,et al.  Restricted, canonical, stereotyped and convergent immunoglobulin responses , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[79]  Johannes Trück,et al.  Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis , 2015, The Journal of Immunology.

[80]  Mark M. Davis,et al.  Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. , 2014, Cell host & microbe.

[81]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[82]  Scott D Boyd,et al.  Convergent antibody signatures in human dengue. , 2013, Cell host & microbe.

[83]  Ning Ma,et al.  IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..

[84]  D. Baker,et al.  Role of conformational sampling in computing mutation‐induced changes in protein structure and stability , 2011, Proteins.

[85]  L. Benatuil,et al.  An improved yeast transformation method for the generation of very large human antibody libraries. , 2010, Protein engineering, design & selection : PEDS.

[86]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[87]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[88]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[89]  K Dane Wittrup,et al.  Isolating and engineering human antibodies using yeast surface display , 2006, Nature Protocols.

[90]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[91]  Edward F. Valeev,et al.  Estimates of the Ab Initio Limit for π−π Interactions: The Benzene Dimer , 2002 .

[92]  F. Gervasio,et al.  Stacking and T-shape competition in aromatic-aromatic amino acid interactions. , 2002, Journal of the American Chemical Society.

[93]  S. Tonegawa,et al.  Sequences of mouse immunoglobulin light chain genes before and after somatic changes , 1978, Cell.

[94]  Susumu Tonegawa,et al.  A complete immunoglobulin gene is created by somatic recombination , 1978, Cell.

[95]  J. Seidman,et al.  Multiple related immunoglobulin variable-region genes identified by cloning and sequence analysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[96]  S. Tonegawa,et al.  Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[97]  Vincent B. Chen,et al.  Acta Crystallographica Section D Biological , 2001 .

[98]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[99]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[100]  R. Brinster,et al.  Somatic hypermutation of an immunoglobulin transgene in K transgenic mice , 1987, Nature.