REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody, Rabbit MAb	Sino Biological	Cat#40588-R001
HRP-conjugated donkey anti rabbit IgG(H + L)	Jackson ImmunoResearch	Cat#711-035-152; RRID:AB_10015282
Ab[numbers]	This study	N/A
BV421 anti-human CD19 Antibody	BioLegend	Cat#302234; RRID:AB_11142678
PE anti-human IgD Antibody	BioLegend	Cat#348204; RRID:AB_10553900
APC/Cy7 anti-human CD27 Antibody	BioLegend	Cat#302816; RRID:AB_571977
PE/Cy7 anti-human CD20 Antibody	BioLegend	Cat#302312; RRID:AB_314260
InVivoMAb human IgG1 Iso-type control	Bio X cell	Cat#BE0297; RRID:AB_2687817
Imdevimab	Hansen et al.16	N/A
Bacterial and virus strains
SARS-CoV-2 JPN/TY/WK-521	National Institute of Infectious Diseases	EPI_ISL_408667
SARS-CoV-2/UT-NCGM02/Human/2020/Tokyo	Imai et al.22	EPI_ISL_418809
SARS-CoV-2 Alpha variant (QHN002)	National Institute of Infectious Diseases	EPI_ISL_804008
SARS-CoV-2 Beta variant (TY8-612)	National Institute of Infectious Diseases	EPI_ISL_1123289
SARS-CoV-2 Gamma variant (TY7-503)	National Institute of Infectious Diseases	EPI_ISL_877769
SARS-CoV-2 Kappa variant (TY11-330)	National Institute of Infectious Diseases	EPI_ISL_2158613
SARS-CoV-2 Delta variant (TY11-927)	National Institute of Infectious Diseases	EPI_ISL_2158617
SARS-CoV-2 Omicron variant (BA.1, TY38-873)	National Institute of Infectious Diseases	EPI_ISL_7418017
SARS-CoV-2 Omicron variant (BA.2, TY40-158)	National Institute of Infectious Diseases	EPI_ISL_9595858
Escherichia coli strain DH5alpha	TOYOBO	Cat#DNA-903F
Chemicals, peptides, and recombinant proteins
RBD-SBP	This paper	N/A
ACE2-SBP	This paper	N/A
ACE2-Flag	This paper	N/A
Polyethylenimine Max	Polyscience	Cat#24765-100
APC-conjugated streptavidin	eBioscience	Cat#17-4317-82
Anti-Aggregate Wash	Cellular Technology Limited	Cat#CTL-AA-010
Buffer RLT	QIAGEN	Cat#79216
2-mercaptoethanol	Thermo Fisher Scientific	Cat#21985023
RNAClean XP	Beckman Coulter	Cat#A63987
dNTP Mix	New England Biolabs	Cat#N0447L
KAPA HiFi HS ReadyMix	KAPA Biosystems	Cat#KK2602
EnduRen	Promega	Cat#E6481
20% formalin	Fujifilm Wako	Cat#064-03865
Cristal violet solution	Merck	Cat#V5265
Opti-MEM I	Thermo Fisher Scientific	Cat#31985070
Blocking One	NACALAI TESQUE	Cat#03953-95
Critical commercial assays
FACS AriaⅢ	BD Biosciences	N/A
FACS Verse	BD Biosciences	N/A
Octet K2	Forte Bio	Cat#Octet K2
Bright-GloTM Luciferase Assay system	Promega	Cat#E2610
GloMax Discover microplate reader	Promega	Cat#GM3000
Epoch 2	Agilent BioTek	Cat#EPOCH2NS
GenElute HP Plasmid Maxiprep Kit	Merck	Cat#NA0300
Expi293 Expression System	Thermo Fisher Scientific	Cat#A14635
BIACORE T200	Cytiva	N/A
Series S Sensor Chip CM5	Cytiva	BR100530
Vitrobot Mark IV system	Thermo Fisher Scientific	N/A
300 kV Titan Krios G4 transmission electron microscope	Thermo Fisher Scientific	N/A
BioQuantum K3 direct electron detector	Gatan	N/A
Quantifoil 0.6/1 Cu 300 mesh	E M Japan	Cat#M2947C-1
rapifleX MALDI Tissuetyper	Bruker Corporation	N/A
StepOnePlus	Thermo Fisher Scientific	Cat#4376598
CFX-96	BIO-RAD	Cat#1854095J1
405 TS washer	Agilent	N/A
Multi-Beads Shocker	YASUI KIKAI	Cat#MB3000
TaqMan Fast Virus 1-step Master Mix	Thermo Fisher Scientific	Cat#4444432
RNeasy Plus Mini Kit	QIAGEN	Cat#74136
HisTrap HP column	Cytiva	Cat#29051021
Superose 6 Increase10/300 GL column	Cytiva	Cat#29091596
Superdex200 10/300 GL column	Cytiva	Cat#28990944
Protein G Sepharose 4 Fast Flow resin	Cytiva	Cat#17061801
HisTrap HP column	Cytiva	Cat#17524801
Streptavidin Biosensors	Sartorius	Cat#18-5019
Anti-human IgG Fc Capture Biosensors	Sartorius	Cat#18-5060
Anti-DYKDDDDK tag Antibody Beads	Fujifilm Wako	Cat#018-22783
Streptavidin Sepharose High Performance	Cytiva	Cat#17511201
NEBuilder HiFi DNA Assembly Master Mix	New England BioLabs	E2621X
Ab Capcher Mag2	Protenova	Cat#P-052-10
Human IgG ELISA Quantitation Set	Bethyl Laboratories	Cat#E80-104
CD19 microbeads	Miltenyi Biotec	Cat#130-050-301
Deposited data
Structure of Ab159 in complex with SARS-CoV-2-RBD	This paper	EMD: 33060 PDB: 7X8Y
Structure of Ab188 in complex with SARS-CoV-2-RBD	This paper	EMD: 33061 PDB: 7X8Z
Structure of Ab326 in complex with SARS-CoV-2-RBD	This paper	EMD: 33062 PDB: 7X90
Structure of Ab354 in complex with SARS-CoV-2-RBD	This paper	EMD: 33059 PDB: 7X8W
Structure of Ab445 in complex with SARS-CoV-2-RBD	This paper	EMD: 33064 PDB: 7X92
Structure of Ab496(Fv-clasp) in complex with SARS-CoV-2-RBD	This paper	EMD: 33063 PDB: 7X91
Experimental models: Cell lines
293T	RIKEN BRC	Cat#RCB2202
Expi293F	Thermo Fisher Scientific	Cat#R79007
293FT cell expressing SARS-CoV-2 Spike and DSP8-11	Yamamoto et al.42	N/A
293FT cell expressing hACE2, hTMPRSS2 and DSP1-7	Yamamoto et al.42	N/A
VeroE6/TMRRSS2 cell	JCRB Cell Bank	Cat#JCRB1819
Raji cells	JCRB Cell Bank	Cat#JCRB9012
Oligonucleotides
SARS-CoV-1-Spike gene optimized	Eurofins Genomics	N/A
Omicron (BA.1)-Spike gene optimized	Eurofins Genomics	N/A
oligo-dT primer (5′-Biotin–AAGCAGT GGTATCAACGCAGAGTACT30VN-3′)	Hokkaido System Science	N/A
2019-nCoV_N1-F primer	Eurofins Genomics	Cat#CDC-01
2019-nCoV_N1-R primer	Eurofins Genomics	Cat#CDC-02
2019-nCoV_N1-P probe	Eurofins Genomics	Cat#CDC-03
Recombinant DNA
pcDNA3.4 TOPO	Thermo Fisher Scientific	Cat#A14697
pcDNA3.4-Spike	Takeshita et al.37	N/A
pcDNA3.4-Spike series	This paper	N/A
pcDNA3.4-ACE2(1-708AA)-SBP	This paper	N/A
pcDNA3.4-ACE2(1-708AA)-Flag	This paper	N/A
pcDNA3.4-Spike(1-1213AA)-SBP	This paper	N/A
pcDNA3.4-S1(1-685AA)-SBP	This paper	N/A
pcDNA3.4-RBD(319-541AA)-SBP	This paper	N/A
pMX-GFP	CELL BIOLABS INC	Cat#RTV-050
pNL4-3.luc.R-E−	NIH	N/A
pCMV3_SARS-cov2d19 series	This paper	N/A
pcDNA3.4-Hexapro	This paper	N/A
pCR2.1- Ab496 Fv-clasp	This paper	N/A
pcDNA3.4-Ab[numbers]-H/L chain	This paper	N/A
Software and algorithms
Octet Data Analysis Software	Sartorius	Version 10.0
FACSuite	BD Biosciences	Version 1.0.6
FACSDiva	BD Biosciences	Version 6.1.3
FlowJo	BD Biosciences	Version 15.0
GraphPad Prism	GraphPad Software	Version 9.3.1
EPU software	Thermo Fisher Scientific	Cat#1025707-J
RELION-3.1.2 package	Zivanov et al.48	N/A
MotionCor2	Zheng et al.50	N/A
CTFFIND4	Rohou and Grigorieff51	N/A
crYOLO	Wagner et al.52	N/A
Phenix package	Liebschner et al.53	N/A
Coot	Emsley et al.54	N/A
SWISS-MODEL server	Waterhouse et al.55	N/A
MolProbity	Williams et al.56	N/A
PyMOL	https://pymol.org/2/	N/A
UCSF ChimeraX	Goddard et al.57	N/A
Mascot	Matrix Science Ltd	Version 2.7
GlyConnect database	Mariethoz et al.59	N/A
JMP	SAS Institute	Version 15.0.0