REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Nanobody C1	Huo et al., 2020a	N/A
Fab	Dejnirattisai et al., 2021a	N/A
IgG	Dejnirattisai et al., 2021a; Liu et al., 2021b	N/A
EY6A mAb	Zhou et al., 2020	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, and Cat#Ly-CoV16
Adagio mAbs	Adagio	Cat#ADG10, Cat#ADG20, and Cat#ADG30
28 mAbs generated from cases of Omicron breakthrough infection	Nutalai et al., 2022	N/A
Anti-c-Myc 9E10 antibody	Biolegend	Catt#626872
Bacterial, virus strains, and yeast
DH5α bacteria	InVitrogen	Cat#18263012
Saccharomyces cerevisiae EBY100	ATCC	Cat#MYA-4941
E. coli clone 10G cells	Lucigen, USA	Cat#60117-1
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., 2021a	N/A
His-tagged SARS-CoV-2/Omicron RBD	This paper	N/A
His-tagged SARS-CoV-2/Omicron BA.4 RBD	This paper	N/A
His-tagged SARS-CoV-2/Omicron BA.5 RBD	This paper	N/A
His-tagged SARS-CoV-2 RBD-62	Zahradník et al., 2021	N/A
His-tagged SARS-CoV-2 RBD N501Y	Supasa et al., 2021	N/A
His-tagged SARS-CoV-2 RBD K417N, E484K, N501Y	Zhou et al., 2021	N/A
His-tagged SARS-CoV-2 RBD K417T, E484K, N501Y	Dejnirattisai et al., 2021b	N/A
His-tagged SARS-CoV-2 RBD L452R, T478K	Liu et al., 2021a	N/A
His-tagged human ACE2	Liu et al., 2021a	N/A
Human ACE2-hIgG1Fc	Liu et al., 2021a	N/A
His-tagged 3C protease	Libby et al., 1988	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
Opti-MEM™	Gibco	Cat#11058021
Fetal Bovine Serum	Gibco	Cat#12676029
Polyethylenimine, branched	Sigma-Aldrich	Cat#408727
Strep-Tactin®XT	IBA Lifesciences	Cat#2-1206-025
HEPES	Melford	Cat#34587-39108
Sodium Chloride	Honeywell	Cat#SZBF3340H
LB broth	Fisher Scientific UK	Cat#51577-51656
Mem Neaa (100X)	Gibco	Cat#2203945
Trypsin-EDTA	Gibco	Cat#2259288
TrypLE™ Express Enzyme	Gibco	Cat#12604013
L-Glutamine 200 mM (100X)	Gibco	Cat#2036885
SYPROorange (5000X in DMSO)	Thermo	Cat#S6651
Isopropyl β-d-1-thiogalactopyranoside	Meridian Bioscience	Cat#BIO-37036
Kanamycin	Melford	Cat#K22000
Lysozyme	Sigma-Aldrich	Cat#L6876
Tris-base	Melford	Cat#T60040
Imidazole	Sigma-Aldrich	Cat#56750
Triton-X-100	Sigma-Aldrich	Cat#8787
Turbonuclease	Sigma-Aldrich	Cat#T4330
RNAse A	Qiagen	Cat#158922
NaCl	Sigma-Aldrich	Cat#S9888
MgSO4	Sigma-Aldrich	Cat#746452
Na2HPO4	Melford	Cat#S23100
NaH2PO4	Melford	Cat#S23185
HBS-EP+ Buffer 10×	Cytiva	Cat# BR100669
Regeneration Solution (glycine-HCl pH 1.7)	Cytiva	Cat# BR100838
Sensor Chip Protein A	Cytiva	Cat#29127555
Biotin CAPture Kit, Series S	Cytiva	CAT#28920234
His-tagged SARS-CoV-2 BA.1 variant RBD	This paper	N/A
His-tagged SARS-CoV-2 BA.2 variant RBD	This paper	N/A
SARS-CoV-2 BA.1 variant Spike	This paper	N/A
SARS-CoV-2 BA.2 variant Spike	This paper	N/A
Streptavidin-APC	Biolegend	Cat# 405207
Streptavidin-APC	Biolegend	Cat# 405207
RNase inhibitor	Promega	Cat# N2611
Protein G Plus/Protein A Agarose	Millipore	Cat#IP10
Pierce™ Fab Preparation Kit	Thermo Fisher	Cat#44985
Twin-Strep-tag® Capture Kit	IBA-Lifesciences	Cat# 2-4370-000
PEGRx 2	Hampton Research	HR2-084
ProPlex™ HT-96	Molecular Dimensions	MD1-42
JCSG-plus™ HT-96	Molecular Dimensions	MD1-40
Critical commercial assays
Bright-Glo Luciferase Assay System	Promega	Cat# E2620
HIV Type 1 p24 Antigen ELISA 2.0	ZeptoMetrix	Cat# 0801002
Deposited data
Crystal structure of SARS-CoV-2 BA.4-RBD/Beta-27 Fab/Nanobody C1 complex	This paper	PDB: 7ZXU
Experimental models: Cell lines
HEK293S GnTI- cells	ATCC	Cat#CRL-3022
HEK293 cells	ATCC	Cat#CRL-3216
Expi293F™ Cells	Gibco,	Cat#A14527
HEK293T/17 cells	ATCC	Cat#CRL-11268™
HEK293T cells	ATCC	Cat#CRL-11268
Hamster: ExpiCHO cells	Thermo Fisher	Cat#A29133
Recombinant DNA
Vector: pHLsec	Aricescu et al., 2006	N/A
Vector: pNEO	Aricescu et al., 2006	N/A
Vector: pHLsec-SARS-CoV-2 spike of BA.1	This paper	N/A
Vector: pTTGneO-SARS-CoV-2 spike of BA.2	This paper	N/A
Vector: pTTGneO-SARS-CoV-2 RBD of BA.2	This paper	N/A
Vector: pNEO-SARS-CoV-2 RBD of BA.1	This paper	N/A
Vector: pCMV-VSV-G	Stewart et al., 2003	Addgene plasmid # 8454
pHR-SIN-ACE2	Alain Townsend	N/A
Vector: pOPING-ET	Nettleship et al., 2008	N/A
Vector: pJYDC1	Adgene	ID: 162458
Vector: p8.91	di Genova et al., 2020	Nigel Temperton
Vector: pCSFLW	di Genova et al., 2020	Nigel Temperton
Vector: pcDNA-SARS-CoV-2 spike of Wuhan strain	di Genova et al., 2020	Nigel Temperton
Vector: pcDNA-SARS-CoV-2 spike of Victoria strain (S247R)	Liu et al., 2021a	N/A
Vector: pcDNA-SARS-CoV-2 spike of Alpha strain (Δ69-70/144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H	Nutalai et al., 2022	N/A
Vector: pcDNA-SARS-CoV-2 spike of Beta strain (L18F, D80A, D215G, Δ242-244, R246I, K417N,E484K, N501Y, D614G, A701V)	Nutalai et al., 2022	N/A
Vector: pcDNA-SARS-CoV-2 spike of Gamma strain (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F)	Nutalai et al., 2022	N/A
Vector: pcDNA-SARS-CoV-2 spike of Delta+A222V strain (T19R, G142D, Del156-157/R158G, A222V, L452R, T478K, D614G, P681R, D950N)	Liu et al., 2021a	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., 2022	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., 2022	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., 2022	N/A
Vector: pcDNA-SARS-CoV-2 spike of BA.3 strain (A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, G339D, S371F, S373P, S375F, D405N, K417N, N440K, G446S, 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.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)	This paper	N/A
TM149 BirA pDisplay	University of Oxford, NDM (C. Siebold)	N/A
Software and algorithms
COOT	Emsley et al., 2010	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Xia2-dials	Winter et al., 2018	https://xia2.github.io
PHENIX	Liebschner et al., 2019	https://www.phenix-online.org/
PyMOL	Warren DeLano and Sarina Bromberg	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/
IBM SPSS Software 27	IBM	https://www.ibm.com
mabscape	This paper	https://snapcraft.io/mabscape
Biacore T200 Evaluation Software 3.1	Cytiva	www.cytivalifesciences.com
Flowjo 10.7.1	BD	https://www.flowjo.com
SnapGene software 5.3.2	Insightful Science	www.snapgene.com
Other
X-ray data were collected at beamline I03, Diamond Light Source, under proposal lb27009 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
QuixStand	GE Healthcare	Cat# 56-4107-78