A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75

. 2022 Dec 14;42(1):111903. doi: 10.1016/j.celrep.2022.111903

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Fab	Dejnirattisai et al.¹⁷	N/A
IgG	Dejnirattisai et al. and Liu et al.¹⁴^,¹⁷	N/A
Human anti-NP (mAb 206)	Dejnirattisai et al.¹⁷	N/A
Regeneron mAbs	AstraZeneca	Cat#REGN10933 and REGN10987
AstraZeneca mAbs	AstraZeneca	Cat#AZD1061, AZD8895 and AZD7442
Vir mAbs	Adagio	Cat#S309
Lilly mAbs	Adagio	Cat#LY-CoV555, LY-CoV16 and LY-CoV1404
Adagio mAbs	Adagio	Cat#ADG10, ADG20 and ADG30
Omicron antibodies	Nutalai et al.²⁰	N/A
Bacterial, Virus Strains, and Yeast	N/A	N/A
DH5α bacteria	In Vitrogen	Cat#18263012

Biological samples

Serum from Pfizer-vaccinated individuals	University of Oxford	N/A
Serum from AstraZeneca-Oxford-vaccinated individuals	University of Oxford	N/A
Plasma from SARS-CoV-2 patients	John Radcliffe Hospital in Oxford UK, South Africa, and FIOCRUZ (WHO) Brazil	N/A

Chemicals, peptides, and recombinant proteins

His-tagged SARS-CoV-2 RBD	Dejnirattisai et al.¹⁷	N/A
His-tagged Avi-tagged SARS-CoV-2/BA.2.75 RBD	This paper	N/A
His-tagged SARS-CoV-2/BA.2 + R493Q RBD	This paper	N/A
His-tagged SARS-CoV-2/BA.2 RBD	Nutalai et al.²⁰	N/A
His-tagged SARS-CoV-2/BA.4/5 RBD	Tuekprakhon et al.¹²	N/A
His-tagged SARS-CoV-2/Alpha RBD	Supasa et al.¹³	N/A
Human ACE2-hIgG1Fc	Liu et al.¹⁴	N/A
Phosphate buffered saline tablets	Sigma-Aldrich	Cat#P4417
Dulbecco’s Modified Eagle Medium, high glucose	Sigma-Aldrich	Cat#D5796
Dulbecco’s Modified Eagle Medium, low glucose	Sigma-Aldrich	Cat#D6046
FreeStyle™ 293 Expression Medium	Gibco	Cat#12338018
L-Glutamine–Penicillin–Streptomycin solution	Sigma-Aldrich	Cat#G1146
GlutaMAX™ Supplement	Gibco	Cat#35050061
UltraDOMA PF Protein-free Medium	Lonza	Cat#12-727F
Opti-MEM™	Gibco	Cat#11058021
Fetal Bovine Serum	Gibco	Cat#12676029
Strep-Tactin®XT	IBA Lifesciences	Cat#2-1206-025
HEPES	Melford	Cat#34587-39108
LB broth	Fisher Scientific UK	Cat#51577-51656
Trypsin-EDTA	Gibco	Cat#2259288
TrypLE™ Express Enzyme	Gibco	Cat#12604013
L-Glutamine 200 mM (100X)	Gibco	Cat#2036885
Isopropyl β-d-1-thiogalactopyranoside	Meridian Bioscience	Cat#BIO-37036
Kanamycin	Melford	Cat#K22000
Ampicillin	Sigma-Aldrich	Cat#PHR2838
Agarose	Sigma-Aldrich	Cat#A2929
SYBR™ Safe DNA Gel Stain	Fisher Scientific UK	Cat#S33102
QIAprep Spin Miniprep Kit	Qiagen	Cat#27106X4
QIAquick® PCR & Gel Cleanup Kit	Qiagen	Cat#28704
Phusion™ High-Fidelity DNA Polymerase	Fisher Scientific UK	Cat#F530S
Bright-Glo™ Luciferase Assay System	Promega	Cat#E2620
HIV1 p24 ELISA Kit	Abcam	Cat#ab218268
NaCl	Sigma-Aldrich	Cat#S9888
Sensor Chip Protein A	Cytiva	Cat#29127555
Biotin CAPture Kit, Series S	Cytiva	CAT#28920234
HBS-EP + Buffer 10×	Cytiva	Cat# BR100669
Regeneration Solution (glycine-HCl pH 1.7)	Cytiva	Cat# BR100838

Deposited data

Crystal structures of SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2	This paper	PDB: 8ASY

Experimental models: Cell lines

HEK293 cells	ATCC	Cat#CRL-3216
Expi293F™ Cells	Gibco,	Cat#A14527
HEK293T/17 cells	ATCC	Cat#CRL-11268™
HEK293T cells	ATCC	Cat#CRL-11268
Vero CCL-81 cells	ATCC	Cat#CCL-81
VeroE6/TMPRSS2 cells	NIBSC	Ref. no. 100978

Recombinant DNA

Vector: pHLsec	Aricescu et al.³⁴	N/A
Vector: pNEO	Aricescu et al.³⁴	N/A
Vector: pHLsec-SARS-CoV-2 spike of Omicron	Nutalai et al.²⁰	N/A
Vector: pOPINTTGneo-BAP-SARS-CoV-2 RBD of BA.2.75	This paper	N/A
Vector: pNEO-SARS-CoV-2 RBD of BA.2	Nutalai et al.²⁰	N/A
Vector: pNEO-SARS-CoV-2 RBD of BA.4/5	Tuekprakhon et al.¹²	N/A
Vector: pNEO-SARS-CoV-2 RBD of BA.2 + R493Q	This paper	N/A
Vector: pNEO-SARS-CoV-2 RBD of Alpha	Supasa et al.¹³	N/A
Vector: pCMV-VSV-G	Stewart et al.³⁵	Addgene plasmid # 8454
pHR-SIN-ACE2	Alain Townsend, Oxford	N/A
Vector: pOPING-ET	Nettleship et al.³⁶	N/A
Vector: pcDNA-SARS-CoV-2 spike of Victoria strain (S247R)	Liu et al.¹⁴	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.1 strain (A67V, Δ69–70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F)	Nutalai et al.²⁰	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.1.1 strain (A67V, Δ69–70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F)	Nutalai et al.²⁰	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2 strain (T19I, Δ24–26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	Nutalai et al.²⁰	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2.12.1 strain (T19I, Δ24–26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y N679K, P681H, S704L, N764K, D796Y, Q954H, N969K)	Nutalai et al.²⁰	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.4/5 strain (T19I, Δ24–26, A27S, Δ69-70, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	Tuekprakhon et al.¹²	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2.75 strain (T19I, Δ24–26, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, D339H, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, R493Q, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	This paper	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2 + D339H strain (T19I, Δ24–26, A27S, G142D, V213G, D339H, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	This paper	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2 + R493Q strain (T19I, Δ24–26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, R493Q, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	This paper	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.2 + G446S strain (T19I, Δ24–26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K)	This paper	N/A
Vector: human IgG1 heavy chain	German Cancer Research Center, Heidelberg, Germany (H. Wardemann	N/A
Vector: human lambda light chain	German Cancer Research Center, Heidelberg, Germany (H. Wardemann	N/A
Vector: human kappa light chain	German Cancer Research Center, Heidelberg, Germany (H. Wardemann	N/A
Vector: Human Fab	Univeristy of Oxford	N/A
Vector: pJYDC1	Adgene	ID: 162,458
TM149 BirA pDisplay	University of Oxford, NDM (C. Siebold)	N/A

Software and algorithms

COOT	Emsley et al.³⁷	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Xia2-dials	Winter et al.³⁸	https://xia2.github.io/parameters.html
PHENIX	Liebschner et al.³⁹	https://www.phenix-online.org/
PyMOL	Warren DeLano,⁴⁰	https://pymol.org/
Data Acquisition Software 11.1.0.11	Fortebio	https://www.fortebio.com/products/octet-systems-software
Data Analysis Software HT 11.1.0.25	Fortebio	https://www.fortebio.com/products/octet-systems-software
Prism 9.0	GraphPad	https://www.graphpad.com/scientific-software/prism/
Yeast display titration curve fitting were done by the standard non-cooperative Hill equation, fitted by nonlinear least-squares regression with two additional parameters using Python 3.7	Zahradnik et al.¹¹	N/A
IBM SPSS Software 27	IBM	https://www.ibm.com
Mabscape	This paper	https://github.com/helenginn/mabscape https://snapcraft.io/mabscape
Biacore T200 Evaluation Software 3.1	Cytiva	www.cytivalifesciences.com

Other

X-ray data were collected at beamline I03, Diamond Light Source, under proposal ib27009 for COVID-19 rapid access	This paper	https://www.diamond.ac.uk/covid-19/for-scientists/rapid-access.html
TALON® Superflow Metal Affinity Resin	Clontech	Cat#635668
HiLoad® 16/600 Superdex® 200 pg	Cytiva	Cat#28-9893-35
Superdex 200 increase 10/300 GL column	Cytiva	Cat#28990944
HisTrap nickel HP 5-mL column	Cytiva	Cat#17524802
HiTrap Heparin HT 5-mL column	Cytiva	Cat#17040703
Amine Reactive Second-Generation (AR2G) Biosensors	Fortebio	Cat#18-5092
Octet RED96e	Fortebio	https://www.fortebio.com/products/label-free-bli-detection/8-channel-octet-systems
Buffer exchange system “QuixStand”	GE Healthcare	Cat#56-4107-78
Cartesian dispensing system	Genomic solutions	Cat#MIC4000
Hydra-96	Robbins Scientific	Cat#Hydra-96
96-well crystallization plate	Greiner bio-one	Cat#E20113NN
Crystallization Imaging System	Formulatrix	Cat#RI-1000
Sonics vibra-cell vcx500 sonicator	VWR	Cat#432-0137
Biacore T200	Cytiva	https://www.cytivalifesciences.com/en/us/shop/protein-analysis/spr-label-free-analysis/systems/biacore-t200-p-05644