Literature DB >> 33621484

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.

Emma C Thomson1, Laura E Rosen2, James G Shepherd3, Roberto Spreafico2, Ana da Silva Filipe3, Jason A Wojcechowskyj2, Chris Davis3, Luca Piccoli4, David J Pascall5, Josh Dillen2, Spyros Lytras3, Nadine Czudnochowski2, Rajiv Shah3, Marcel Meury2, Natasha Jesudason3, Anna De Marco4, Kathy Li3, Jessica Bassi4, Aine O'Toole6, Dora Pinto4, Rachel M Colquhoun6, Katja Culap4, Ben Jackson6, Fabrizia Zatta4, Andrew Rambaut6, Stefano Jaconi4, Vattipally B Sreenu3, Jay Nix7, Ivy Zhang8, Ruth F Jarrett3, William G Glass9, Martina Beltramello4, Kyriaki Nomikou3, Matteo Pizzuto4, Lily Tong3, Elisabetta Cameroni4, Tristan I Croll10, Natasha Johnson3, Julia Di Iulio2, Arthur Wickenhagen3, Alessandro Ceschi11, Aoife M Harbison12, Daniel Mair3, Paolo Ferrari13, Katherine Smollett3, Federica Sallusto14, Stephen Carmichael3, Christian Garzoni15, Jenna Nichols3, Massimo Galli16, Joseph Hughes3, Agostino Riva16, Antonia Ho3, Marco Schiuma16, Malcolm G Semple17, Peter J M Openshaw18, Elisa Fadda12, J Kenneth Baillie19, John D Chodera9, Suzannah J Rihn3, Samantha J Lycett20, Herbert W Virgin21, Amalio Telenti2, Davide Corti4, David L Robertson22, Gyorgy Snell23.   

Abstract

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  COVID-19; N439K; SARS-CoV-2; Spike; monoclonal antibody escape; mutation; protein structure; receptor binding motif; variant

Mesh:

Substances:

Year:  2021        PMID: 33621484      PMCID: PMC7843029          DOI: 10.1016/j.cell.2021.01.037

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   66.850


  81 in total

1.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.

Authors:  Daniel Wrapp; Nianshuang Wang; Kizzmekia S Corbett; Jory A Goldsmith; Ching-Lin Hsieh; Olubukola Abiona; Barney S Graham; Jason S McLellan
Journal:  Science       Date:  2020-02-19       Impact factor: 47.728

2.  Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.

Authors:  Yiska Weisblum; Fabian Schmidt; Fengwen Zhang; Justin DaSilva; Daniel Poston; Julio Cc Lorenzi; Frauke Muecksch; Magdalena Rutkowska; Hans-Heinrich Hoffmann; Eleftherios Michailidis; Christian Gaebler; Marianna Agudelo; Alice Cho; Zijun Wang; Anna Gazumyan; Melissa Cipolla; Larry Luchsinger; Christopher D Hillyer; Marina Caskey; Davide F Robbiani; Charles M Rice; Michel C Nussenzweig; Theodora Hatziioannou; Paul D Bieniasz
Journal:  Elife       Date:  2020-10-28       Impact factor: 8.140

3.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

4.  UCSF ChimeraX: Structure visualization for researchers, educators, and developers.

Authors:  Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Elaine C Meng; Gregory S Couch; Tristan I Croll; John H Morris; Thomas E Ferrin
Journal:  Protein Sci       Date:  2020-10-22       Impact factor: 6.993

5.  An integrated national scale SARS-CoV-2 genomic surveillance network.

Authors: 
Journal:  Lancet Microbe       Date:  2020-06-02

6.  Convergent antibody responses to SARS-CoV-2 in convalescent individuals.

Authors:  Davide F Robbiani; Christian Gaebler; Frauke Muecksch; Julio C C Lorenzi; Zijun Wang; Alice Cho; Marianna Agudelo; Christopher O Barnes; Anna Gazumyan; Shlomo Finkin; Thomas Hägglöf; Thiago Y Oliveira; Charlotte Viant; Arlene Hurley; Hans-Heinrich Hoffmann; Katrina G Millard; Rhonda G Kost; Melissa Cipolla; Kristie Gordon; Filippo Bianchini; Spencer T Chen; Victor Ramos; Roshni Patel; Juan Dizon; Irina Shimeliovich; Pilar Mendoza; Harald Hartweger; Lilian Nogueira; Maggi Pack; Jill Horowitz; Fabian Schmidt; Yiska Weisblum; Eleftherios Michailidis; Alison W Ashbrook; Eric Waltari; John E Pak; Kathryn E Huey-Tubman; Nicholas Koranda; Pauline R Hoffman; Anthony P West; Charles M Rice; Theodora Hatziioannou; Pamela J Bjorkman; Paul D Bieniasz; Marina Caskey; Michel C Nussenzweig
Journal:  Nature       Date:  2020-06-18       Impact factor: 69.504

7.  Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies.

Authors:  Daniel Wrapp; Dorien De Vlieger; Kizzmekia S Corbett; Gretel M Torres; Nianshuang Wang; Wander Van Breedam; Kenny Roose; Loes van Schie; Markus Hoffmann; Stefan Pöhlmann; Barney S Graham; Nico Callewaert; Bert Schepens; Xavier Saelens; Jason S McLellan
Journal:  Cell       Date:  2020-05-05       Impact factor: 41.582

8.  The influenza virus hemagglutinin head evolves faster than the stalk domain.

Authors:  Ericka Kirkpatrick; Xueting Qiu; Patrick C Wilson; Justin Bahl; Florian Krammer
Journal:  Sci Rep       Date:  2018-07-11       Impact factor: 4.379

9.  Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.

Authors:  Johanna Hansen; Alina Baum; Kristen E Pascal; Vincenzo Russo; Stephanie Giordano; Elzbieta Wloga; Benjamin O Fulton; Ying Yan; Katrina Koon; Krunal Patel; Kyung Min Chung; Aynur Hermann; Erica Ullman; Jonathan Cruz; Ashique Rafique; Tammy Huang; Jeanette Fairhurst; Christen Libertiny; Marine Malbec; Wen-Yi Lee; Richard Welsh; Glen Farr; Seth Pennington; Dipali Deshpande; Jemmie Cheng; Anke Watty; Pascal Bouffard; Robert Babb; Natasha Levenkova; Calvin Chen; Bojie Zhang; Annabel Romero Hernandez; Kei Saotome; Yi Zhou; Matthew Franklin; Sumathi Sivapalasingam; David Chien Lye; Stuart Weston; James Logue; Robert Haupt; Matthew Frieman; Gang Chen; William Olson; Andrew J Murphy; Neil Stahl; George D Yancopoulos; Christos A Kyratsous
Journal:  Science       Date:  2020-06-15       Impact factor: 47.728

Review 10.  Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting.

Authors:  Fran Robson; Khadija Shahed Khan; Thi Khanh Le; Clément Paris; Sinem Demirbag; Peter Barfuss; Palma Rocchi; Wai-Lung Ng
Journal:  Mol Cell       Date:  2020-08-04       Impact factor: 17.970

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  218 in total

1.  Bioinformatics for the Origin and Evolution of Viruses.

Authors:  Jiajia Chen; Yuxin Zhang; Bairong Shen
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

2.  SARS-CoV-2 Variants: A Synopsis of In Vitro Efficacy Data of Convalescent Plasma, Currently Marketed Vaccines, and Monoclonal Antibodies.

Authors:  Daniele Focosi; Marco Tuccori; Andreina Baj; Fabrizio Maggi
Journal:  Viruses       Date:  2021-06-23       Impact factor: 5.048

3.  Nasal delivery of an IgM offers broad protection from SARS-CoV-2 variants.

Authors:  Zhiqiang Ku; Xuping Xie; Paul R Hinton; Xinli Liu; Xiaohua Ye; Antonio E Muruato; Dean C Ng; Sujit Biswas; Jing Zou; Yang Liu; Deepal Pandya; Vineet D Menachery; Sachi Rahman; Yu-An Cao; Hui Deng; Wei Xiong; Kevin B Carlin; Junquan Liu; Hang Su; Elizabeth J Haanes; Bruce A Keyt; Ningyan Zhang; Stephen F Carroll; Pei-Yong Shi; Zhiqiang An
Journal:  Nature       Date:  2021-06-03       Impact factor: 49.962

4.  A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity.

Authors:  Ren Yang; Yao Deng; Baoying Huang; Lei Huang; Ang Lin; Yuhua Li; Wenling Wang; Jingjing Liu; Shuaiyao Lu; Zhenzhen Zhan; Yufei Wang; Ruhan A; Wen Wang; Peihua Niu; Li Zhao; Shiqiang Li; Xiaopin Ma; Luyao Zhang; Yujian Zhang; Weiguo Yao; Xingjie Liang; Jincun Zhao; Zhongmin Liu; Xiaozhong Peng; Hangwen Li; Wenjie Tan
Journal:  Signal Transduct Target Ther       Date:  2021-05-31

5.  Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses.

Authors:  Sham Nambulli; Yufei Xiang; Natasha L Tilston-Lunel; Linda J Rennick; Zhe Sang; William B Klimstra; Douglas S Reed; Nicholas A Crossland; Yi Shi; W Paul Duprex
Journal:  Sci Adv       Date:  2021-05-26       Impact factor: 14.136

Review 6.  Fast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines.

Authors:  Weilin Zhou; Wei Wang
Journal:  Signal Transduct Target Ther       Date:  2021-06-09

7.  Highly conserved, non-human-like, and cross-reactive SARS-CoV-2 T cell epitopes for COVID-19 vaccine design and validation.

Authors:  Lauren M Meyers; Andres H Gutiérrez; Christine M Boyle; Frances Terry; Bethany G McGonnigal; Andres Salazar; Michael F Princiotta; Wiliam D Martin; Anne S De Groot; Leonard Moise
Journal:  NPJ Vaccines       Date:  2021-05-13       Impact factor: 7.344

8.  SARS-CoV-2 within-host diversity and transmission.

Authors:  Katrina A Lythgoe; Matthew Hall; Luca Ferretti; Mariateresa de Cesare; George MacIntyre-Cockett; Amy Trebes; Monique Andersson; Newton Otecko; Emma L Wise; Nathan Moore; Jessica Lynch; Stephen Kidd; Nicholas Cortes; Matilde Mori; Rebecca Williams; Gabrielle Vernet; Anita Justice; Angie Green; Samuel M Nicholls; M Azim Ansari; Lucie Abeler-Dörner; Catrin E Moore; Timothy E A Peto; David W Eyre; Robert Shaw; Peter Simmonds; David Buck; John A Todd; Thomas R Connor; Shirin Ashraf; Ana da Silva Filipe; James Shepherd; Emma C Thomson; David Bonsall; Christophe Fraser; Tanya Golubchik
Journal:  Science       Date:  2021-03-09       Impact factor: 47.728

9.  Hospital mortality in COVID-19 patients in Belgium treated with statins, ACE inhibitors and/or ARBs.

Authors:  Geert Byttebier; Luc Belmans; Myriam Alexander; Bo E H Saxberg; Bart De Spiegeleer; Anton De Spiegeleer; Nick Devreker; Jens T Van Praet; Karolien Vanhove; Reinhilde Reybrouck; Evelien Wynendaele; David S Fedson
Journal:  Hum Vaccin Immunother       Date:  2021-05-28       Impact factor: 3.452

Review 10.  SARS-CoV-2 variants, spike mutations and immune escape.

Authors:  William T Harvey; Alessandro M Carabelli; Ben Jackson; Ravindra K Gupta; Emma C Thomson; Ewan M Harrison; Catherine Ludden; Richard Reeve; Andrew Rambaut; Sharon J Peacock; David L Robertson
Journal:  Nat Rev Microbiol       Date:  2021-06-01       Impact factor: 78.297

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