Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition.
Angiotensin-Converting Enzyme 2
/ chemistry
Antibodies, Monoclonal
/ immunology
Antibodies, Neutralizing
/ immunology
Binding Sites
Epitopes
/ immunology
Gene Library
High-Throughput Nucleotide Sequencing
Humans
Protein Domains
SARS-CoV-2
/ genetics
Saccharomyces cerevisiae
/ genetics
Spike Glycoprotein, Coronavirus
/ chemistry
SARS-CoV-2
antibody escape
antigenic evolution
deep mutational scanning
Journal
Cell host & microbe
ISSN: 1934-6069
Titre abrégé: Cell Host Microbe
Pays: United States
ID NLM: 101302316
Informations de publication
Date de publication:
13 01 2021
13 01 2021
Historique:
received:
11
09
2020
revised:
19
10
2020
accepted:
13
11
2020
pubmed:
2
12
2020
medline:
21
1
2021
entrez:
1
12
2020
Statut:
ppublish
Résumé
Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies. They further enable the design of escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same RBD surface but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
Identifiants
pubmed: 33259788
pii: S1931-3128(20)30624-7
doi: 10.1016/j.chom.2020.11.007
pmc: PMC7676316
pii:
doi:
Substances chimiques
Antibodies, Monoclonal
0
Antibodies, Neutralizing
0
Epitopes
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
ACE2 protein, human
EC 3.4.17.23
Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
44-57.e9Subventions
Organisme : NIAID NIH HHS
ID : 75N93019C00074
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI140891
Pays : United States
Organisme : NIAID NIH HHS
ID : 75N93019C00062
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI150739
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI127893
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI141707
Pays : United States
Organisme : NIAID NIH HHS
ID : F30 AI149928
Pays : United States
Organisme : NIAID NIH HHS
ID : T32 AI083203
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests J.E.C. has served as a consultant for Sanofi, is on the Scientific Advisory Boards of CompuVax and Meissa Vaccines, is a recipient of previous unrelated grants from Moderna and Sanofi, and is a founder of IDBiologics. Vanderbilt University has applied for patents on SARS-CoV-2 antibodies. S.P.J.W. and P.W.R. have filed a disclosure with Washington University for recombinant VSV. The other authors declare no competing interests.
Références
Cell Host Microbe. 2020 Sep 9;28(3):486-496.e6
pubmed: 32738193
Nat Biomed Eng. 2020 Nov;4(11):1030-1043
pubmed: 32747832
Nat Methods. 2017 Mar;14(3):290-296
pubmed: 28165473
Science. 2020 Aug 7;369(6504):650-655
pubmed: 32571838
Science. 2020 Aug 7;369(6504):731-736
pubmed: 32540900
Nature. 2020 Aug;584(7819):115-119
pubmed: 32454513
Cell. 2020 Sep 3;182(5):1295-1310.e20
pubmed: 32841599
J Mol Biol. 1993 Dec 5;234(3):554-63
pubmed: 7504735
Viruses. 2020 Sep 05;12(9):
pubmed: 32899480
J Virol. 2014 Jun;88(12):7070-82
pubmed: 24719429
Emerg Microbes Infect. 2020 Dec;9(1):382-385
pubmed: 32065055
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Science. 2020 Mar 13;367(6483):1260-1263
pubmed: 32075877
J Immunol. 2020 Aug 15;205(4):915-922
pubmed: 32591393
Elife. 2020 Oct 28;9:
pubmed: 33112236
Nat Methods. 2019 Nov;16(11):1153-1160
pubmed: 31591578
Nat Med. 2020 Sep;26(9):1422-1427
pubmed: 32651581
Cell. 2020 Nov 25;183(5):1367-1382.e17
pubmed: 33160446
Cell. 2020 Jul 9;182(1):73-84.e16
pubmed: 32425270
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Cell. 2020 Feb 6;180(3):471-489.e22
pubmed: 32004464
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Elife. 2019 Aug 27;8:
pubmed: 31452511
Nat Biotechnol. 2013 Jun;31(6):545-52
pubmed: 23685480
J Clin Microbiol. 2020 Oct 21;58(11):
pubmed: 32826322
Nature. 2020 Aug;584(7821):450-456
pubmed: 32698192
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Cell. 2015 May 21;161(5):1026-1034
pubmed: 25959776
Science. 2004 Jul 16;305(5682):371-6
pubmed: 15218094
Cell. 2020 Aug 6;182(3):744-753.e4
pubmed: 32553273
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Cell Host Microbe. 2019 Jan 9;25(1):39-48.e5
pubmed: 30629917
Science. 2020 Sep 18;369(6510):1501-1505
pubmed: 32703906
Immunity. 2019 Feb 19;50(2):520-532.e3
pubmed: 30709739
Nat Commun. 2020 Oct 15;11(1):5208
pubmed: 33060581
Science. 2020 May 8;368(6491):630-633
pubmed: 32245784
Bioinformatics. 2006 Nov 1;22(21):2695-6
pubmed: 16940322
Science. 2020 Aug 21;369(6506):1014-1018
pubmed: 32540904
Biochemistry. 1998 Jun 2;37(22):7981-91
pubmed: 9609690
Cell Host Microbe. 2020 Sep 9;28(3):445-454.e6
pubmed: 32585135
Nature. 2020 May;581(7807):221-224
pubmed: 32225175
PLoS Med. 2006 Jul;3(7):e237
pubmed: 16796401
Hum Vaccin Immunother. 2014;10(3):648-58
pubmed: 24355931
Nature. 2020 Jul;583(7815):282-285
pubmed: 32218527
Science. 2020 Aug 21;369(6506):956-963
pubmed: 32540903
Cell Host Microbe. 2020 Sep 9;28(3):475-485.e5
pubmed: 32735849
J Virol. 2015 Dec 30;90(6):3253-6
pubmed: 26719272
Science. 2020 Nov 27;370(6520):1110-1115
pubmed: 33037066
Nat Microbiol. 2020 Apr;5(4):562-569
pubmed: 32094589
Am J Epidemiol. 1973 Jun;97(6):365-71
pubmed: 4713932
Nat Biotechnol. 2018 Dec 03;:
pubmed: 30531897
J Open Source Softw. 2020;5(52):
pubmed: 34189395
Immunity. 2020 Feb 18;52(2):388-403.e12
pubmed: 32023489
Science. 2020 Jun 12;368(6496):1274-1278
pubmed: 32404477
J Mol Biol. 1992 Aug 5;226(3):851-65
pubmed: 1380563
Biol Proced Online. 2004;6:23-34
pubmed: 15103397
Science. 2020 Nov 20;370(6519):950-957
pubmed: 32972994
Nature. 2020 Aug;584(7821):443-449
pubmed: 32668443
J Struct Biol. 2005 Oct;152(1):36-51
pubmed: 16182563
Emerg Infect Dis. 2009 Mar;15(3):482-5
pubmed: 19239771
J Virol. 2004 Mar;78(5):2581-5
pubmed: 14963161
Appl Environ Microbiol. 2007 Feb;73(4):1189-98
pubmed: 17189442
Science. 2005 Sep 16;309(5742):1864-8
pubmed: 16166518
Cell Host Microbe. 2021 Jan 13;29(1):23-31.e4
pubmed: 33306985
Cell. 2020 Sep 3;182(5):1284-1294.e9
pubmed: 32730807
Nature. 2020 Dec;588(7839):682-687
pubmed: 33045718
Immunity. 2020 Jul 14;53(1):98-105.e5
pubmed: 32561270
Nat Commun. 2017 Nov 23;8(1):1735
pubmed: 29170370
Curr Biol. 2020 Jun 8;30(11):2196-2203.e3
pubmed: 32416074
Science. 2003 Aug 29;301(5637):1244-6
pubmed: 12947202
Science. 1995 Jan 20;267(5196):383-6
pubmed: 7529940
Science. 2020 Aug 7;369(6504):643-650
pubmed: 32540902
Cell. 2020 Nov 12;183(4):1024-1042.e21
pubmed: 32991844
J Mol Biol. 1998 Jul 3;280(1):1-9
pubmed: 9653027
Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):E7550-E7558
pubmed: 30037990
Nature. 1970 Feb 7;225(5232):563-4
pubmed: 5411867
Nat Commun. 2020 Sep 1;11(1):4378
pubmed: 32873791
J Infect Dis. 2021 Feb 3;223(2):197-205
pubmed: 33535236
Viruses. 2020 May 06;12(5):
pubmed: 32384820
Nature. 2020 May;581(7807):215-220
pubmed: 32225176
Sci Transl Med. 2017 Sep 20;9(408):
pubmed: 28931655