An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

Liu, Lihong; Iketani, Sho; Guo, Yicheng; Reddem, Eswar R.; Casner, Ryan G.; Nair, Manoj S.; Yu, Jian; Chan, Jasper F.-W.; Wang, Maple; Cerutti, Gabriele; Li, Zhiteng; Morano, Nicholas C.; Castagna, Candace D.; Corredor, Laura; Chu, Hin; Yuan, Shuofeng; Poon, Vincent Kwok-Man; Chan, Chris Chun-Sing; Chen, Zhiwei; Luo, Yang; Cunningham, Marcus; Chavez, Alejandro; Yin, Michael T.; Perlin, David S.; Tsuji, Moriya; Yuen, Kwok-Yung; Kwong, Peter D.; Sheng, Zizhang; Huang, Yaoxing; Shapiro, Lawrence; Ho, David D.

doi:10.1126/scitranslmed.abn6859

Title: An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

Journal Article · Tue Apr 19 00:00:00 EDT 2022 · Science Translational Medicine

DOI:https://doi.org/10.1126/scitranslmed.abn6859· OSTI ID:1871706

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Columbia Univ., New York, NY (United States)
Univ. of Hong Kong, Hong Kong Special Administrative Region (China); Health@InnoHK, Hong Kong Special Administrative Region (China): Columbia Univ., New York, NY (United States)
Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ (United States); Hackensack Meridian School of Medicine, Nutley, NJ (United States)
Health@InnoHK, Hong Kong Special Administrative Region (China): Columbia Univ., New York, NY (United States)
Columbia Univ., New York, NY (United States); National Institutes of Health (NIH), Bethesda, MD (United States)

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)

Grant/Contract Number:: W-31-109-Eng-38

OSTI ID:: 1871706

Alternate ID(s):: OSTI ID: 1872615

Journal Information:: Science Translational Medicine, Vol. 14, Issue 646; ISSN 1946-6234

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (60)

Anti-SARS-CoV-2 receptor-binding domain antibody evolution after mRNA vaccination Cho, Alice; Muecksch, Frauke; Schaefer-Babajew, Dennis Nature, Vol. 600, Issue 7889 https://doi.org/10.1038/s41586-021-04060-7	journal	October 2021
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Davis, I. W.; Murray, L. W.; Richardson, J. S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh398	journal	July 2004
Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice Martinez, David R.; Schäfer, Alexandra; Leist, Sarah R. Science, Vol. 373, Issue 6558 https://doi.org/10.1126/science.abi4506	journal	August 2021
Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class Rapp, Micah; Guo, Yicheng; Reddem, Eswar R. Cell Reports, Vol. 35, Issue 1 https://doi.org/10.1016/j.celrep.2021.108950	journal	April 2021
Solving structures of protein complexes by molecular replacement with Phaser McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1 https://doi.org/10.1107/S0907444906045975	journal	December 2006
In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies Li, Dapeng; Edwards, Robert J.; Manne, Kartik Cell, Vol. 184, Issue 16 https://doi.org/10.1016/j.cell.2021.06.021	journal	August 2021
The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus Wells, H. L.; Letko, M.; Lasso, G. Virus Evolution, Vol. 7, Issue 1 https://doi.org/10.1093/ve/veab007	journal	January 2021
Lethal Infection of K18- hACE2 Mice Infected with Severe Acute Respiratory Syndrome Coronavirus McCray, Paul B.; Pewe, Lecia; Wohlford-Lenane, Christine Journal of Virology, Vol. 81, Issue 2 https://doi.org/10.1128/JVI.02012-06	journal	January 2007
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants Wang, Zijun; Schmidt, Fabian; Weisblum, Yiska Nature, Vol. 592, Issue 7855 https://doi.org/10.1038/s41586-021-03324-6	journal	February 2021
Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant Graham, Carl; Seow, Jeffrey; Huettner, Isabella Immunity, Vol. 54, Issue 6 https://doi.org/10.1016/j.immuni.2021.03.023	journal	June 2021
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants Xu, Jianliang; Xu, Kai; Jung, Seolkyoung Nature, Vol. 595, Issue 7866 https://doi.org/10.1038/s41586-021-03676-z	journal	June 2021
Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses Ladner, Jason T.; Henson, Sierra N.; Boyle, Annalee S. Cell Reports Medicine, Vol. 2, Issue 1 https://doi.org/10.1016/j.xcrm.2020.100189	journal	January 2021
A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV Yuan, Meng; Wu, Nicholas C.; Zhu, Xueyong Science, Vol. 368, Issue 6491 https://doi.org/10.1126/science.abb7269	journal	April 2020
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C. Science, Vol. 372, Issue 6538 https://doi.org/10.1126/science.abg3055	journal	March 2021
Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection Wang, Zijun; Muecksch, Frauke; Schaefer-Babajew, Dennis Nature, Vol. 595, Issue 7867 https://doi.org/10.1038/s41586-021-03696-9	journal	June 2021
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 Wang, Pengfei; Nair, Manoj S.; Liu, Lihong Nature, Vol. 593, Issue 7857 https://doi.org/10.1038/s41586-021-03398-2	journal	March 2021
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2 Liu, Lihong; Iketani, Sho; Guo, Yicheng Nature, Vol. 602, Issue 7898 https://doi.org/10.1038/s41586-021-04388-0	journal	December 2021
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies Barnes, Christopher O.; Jette, Claudia A.; Abernathy, Morgan E. Nature, Vol. 588, Issue 7839 https://doi.org/10.1038/s41586-020-2852-1	journal	October 2020
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S. Science, Vol. 367, Issue 6483 https://doi.org/10.1126/science.abb2507	journal	February 2020
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice Cohen, Alexander A.; Gnanapragasam, Priyanthi N. P.; Lee, Yu E. Science, Vol. 371, Issue 6530 https://doi.org/10.1126/science.abf6840	journal	February 2021
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts Schramm, Chaim A.; Sheng, Zizhang; Zhang, Zhenhai Frontiers in Immunology, Vol. 7 https://doi.org/10.3389/fimmu.2016.00372	journal	September 2016
Broad sarbecovirus neutralization by a human monoclonal antibody Tortorici, M. Alejandra; Czudnochowski, Nadine; Starr, Tyler N. Nature, Vol. 597, Issue 7874 https://doi.org/10.1038/s41586-021-03817-4	journal	July 2021
Disease X: accelerating the development of medical countermeasures for the next pandemic Simpson, Shmona; Kaufmann, Michael C.; Glozman, Vitaly The Lancet Infectious Diseases, Vol. 20, Issue 5 https://doi.org/10.1016/S1473-3099(20)30123-7	journal	May 2020
A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses Wang, Pengfei; Casner, Ryan G.; Nair, Manoj S. Emerging Microbes & Infections, Vol. 11, Issue 1 https://doi.org/10.1080/22221751.2021.2011623	journal	December 2021
Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity Liu, Hejun; Wu, Nicholas C.; Yuan, Meng Immunity, Vol. 53, Issue 6 https://doi.org/10.1016/j.immuni.2020.10.023	journal	December 2020
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies Copin, Richard; Baum, Alina; Wloga, Elzbieta Cell, Vol. 184, Issue 15 https://doi.org/10.1016/j.cell.2021.06.002	journal	July 2021
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Evolution of antibody immunity to SARS-CoV-2 Gaebler, Christian; Wang, Zijun; Lorenzi, Julio C. C. Nature, Vol. 591, Issue 7851 https://doi.org/10.1038/s41586-021-03207-w	journal	January 2021
A Mouse-Adapted SARS-CoV-2 Induces Acute Lung Injury and Mortality in Standard Laboratory Mice Leist, Sarah R.; Dinnon, Kenneth H.; Schäfer, Alexandra Cell, Vol. 183, Issue 4 https://doi.org/10.1016/j.cell.2020.09.050	journal	November 2020
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape Starr, Tyler N.; Czudnochowski, Nadine; Liu, Zhuoming Nature https://doi.org/10.1038/s41586-021-03807-6	journal	July 2021
Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines Walls, Alexandra C.; Miranda, Marcos C.; Schäfer, Alexandra Cell, Vol. 184, Issue 21 https://doi.org/10.1016/j.cell.2021.09.015	journal	October 2021
Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody Rappazzo, C. Garrett; Tse, Longping V.; Kaku, Chengzi I. Science, Vol. 371, Issue 6531 https://doi.org/10.1126/science.abf4830	journal	February 2021
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies Wrapp, Daniel; De Vlieger, Dorien; Corbett, Kizzmekia S. Cell, Vol. 181, Issue 5 https://doi.org/10.1016/j.cell.2020.04.031	journal	May 2020
GISAID: Global initiative on sharing all influenza data – from vision to reality Shu, Yuelong; McCauley, John Eurosurveillance, Vol. 22, Issue 13 https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494	journal	March 2017
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic Boni, Maciej F.; Lemey, Philippe; Jiang, Xiaowei Nature Microbiology, Vol. 5, Issue 11 https://doi.org/10.1038/s41564-020-0771-4	journal	July 2020
Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays Crawford, Katharine H. D.; Eguia, Rachel; Dingens, Adam S. Viruses, Vol. 12, Issue 5 https://doi.org/10.3390/v12050513	journal	May 2020
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study Chu, Hin; Chan, Jasper Fuk-Woo; Yuen, Terrence Tsz-Tai The Lancet Microbe, Vol. 1, Issue 1 https://doi.org/10.1016/S2666-5247(20)30004-5	journal	May 2020
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies Cao, Yunlong; Wang, Jing; Jian, Fanchong Nature, Vol. 602, Issue 7898 https://doi.org/10.1038/s41586-021-04385-3	journal	December 2021
Bamlanivimab plus Etesevimab in Mild or Moderate Covid-19 Dougan, Michael; Nirula, Ajay; Azizad, Masoud New England Journal of Medicine, Vol. 385, Issue 15 https://doi.org/10.1056/NEJMoa2102685	journal	October 2021
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro Molecular Biology and Evolution, Vol. 33, Issue 7 https://doi.org/10.1093/molbev/msw054	journal	March 2016
cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence Guo, Yicheng; Chen, Kevin; Kwong, Peter D. Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02365	journal	October 2019
An interactive web-based dashboard to track COVID-19 in real time Dong, Ensheng; Du, Hongru; Gardner, Lauren The Lancet Infectious Diseases, Vol. 20, Issue 5 https://doi.org/10.1016/S1473-3099(20)30120-1	journal	May 2020
REGN-COV2, a Neutralizing Antibody Cocktail, in Outpatients with Covid-19 Weinreich, David M.; Sivapalasingam, Sumathi; Norton, Thomas New England Journal of Medicine, Vol. 384, Issue 3 https://doi.org/10.1056/NEJMoa2035002	journal	January 2021
Convergent antibody responses to SARS-CoV-2 in convalescent individuals Robbiani, Davide F.; Gaebler, Christian; Muecksch, Frauke Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2456-9	journal	June 2020
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
SAbPred: a structure-based antibody prediction server Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw361	journal	April 2016
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Pinto, Dora; Park, Young-Jun; Beltramello, Martina Nature, Vol. 583, Issue 7815 https://doi.org/10.1038/s41586-020-2349-y	journal	May 2020
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Automated electron microscope tomography using robust prediction of specimen movements Mastronarde, David N. Journal of Structural Biology, Vol. 152, Issue 1 https://doi.org/10.1016/j.jsb.2005.07.007	journal	October 2005
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike Liu, Lihong; Wang, Pengfei; Nair, Manoj S. Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2571-7	journal	July 2020
The PDB_REDO server for macromolecular structure model optimization Joosten, Robbie P.; Long, Fei; Murshudov, Garib N. IUCrJ, Vol. 1, Issue 4 https://doi.org/10.1107/S2052252514009324	journal	May 2014
Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability Brouwer, Philip J. M.; Caniels, Tom G.; van der Straten, Karlijn Science, Vol. 369, Issue 6504 https://doi.org/10.1126/science.abc5902	journal	June 2020

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