REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Biotin CD3 Monoclonal Antibody (UCHT1)	eBioscience	Cat#13-0038-82, RRID:AB_466323
Biotin Mouse Anti-Human CD8 (RPA-T8)	BD	Cat#555365; RRID:AB_395768
Biotin CD14 Monoclonal Antibody (61D3)	eBioscience	Cat#13-0149-82; RRID:AB_466373
Anti-human CD19 Antibody FITC (HIB19)	BioLegend	Cat#302206; RRID:AB_314236
Anti-human IgM Antibody APC/Cy7 (MHM-88)	BioLegend	Cat#314520; RRID:AB_10900422
Anti-Human IgG BV421 (G18-145)	BD	Cat#562581; RRID:AB_2737665
anti-human CD27 Antibody PE (M-T271)	BioLegend	Cat#356406; RRID:AB_2561825
APC-conjugated AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG (H + L)	Jackson ImmunoResearch	Cat#109-136-088; RRID:AB_2337691
Bacterial and virus strains
SARS-CoV-2 Japan/NGS-IA-1/2020	Sakurai et al., 2021	GISAID ID number: EPI_ISL_481251
SARS-CoV-2 Japan/TY7-503/2021	National Institute of Infectious Diseases, Japan	GISAID ID number: EPI_ISL_877769
SARS-CoV-2 Japan/TY8-612-P1/2021	National Institute of Infectious Diseases, Japan	GISAID ID number: EPI_ISL_1123289
SARS-CoV-2 Japan/QK002/2020	National Institute of Infectious Diseases, Japan	GISAID ID number: EPI_ISL_768526
Stbl2 Competent Cells	Invitrogen	Cat#10268019
Biological samples
Blood of SARS-CoV-2 infected patient A and B, See Table S1	This paper	N/A
Plasma of SARS-CoV-2 infected individuals, See Table S2	This paper	N/A
Chemicals, peptides, and recombinant proteins
MojoSort Magnet	BioLegend	Cat#480019
7AAD	BD	Cat#559925
guanidine thiocyanate	Invitrogen	Cat#AM9422
dNTP-Mix (10mM)	Invitrogen	Cat#18427088
Recombinant RNase inhibitor	Takara	Cat#2313B
Superscript III reverse transcriptase	Invitrogen	Cat#18080085
Sensor Chip CM5	cytiva	Cat#BR100030
Human Antibody Capture Kit	cytiva	Cat#BR100839
Amine Coupling Kit	cytiva	Cat#BR100050
G418	Millipore	Cat#345812-20ML
Hygromycin B	Nacalai Tesque	Cat#09287-84
RBD	This paper	N/A
NTD	This paper	N/A
Protein A AlphaScreen Donor Beads	PerkinElmer	Cat#AS102D
Anti-His AlphaLISA Acceptor beads	PerkinElmer	Cat#AL178C
Carboxymethyl cellulose	Sigma	Cat#C9481-500G
Methylene blue	Nacalai Tesque	Cat#22412-14
Critical commercial assays
FectoPRO	Polyplus-transfection	Cat#116-010
FectoCHO Expression System	Polyplus-transfection	Cat#716-06LKIT
Luciferase assay system	Promega	Cat#E4550
EnduRen	Promega	Cat#E6481
Gibson Assembly Master Mix	New England Biolabs	Cat#E2611L
HiTrap rProtein A FF Column	cytiva	Cat#17507901
COSMOGEL His-Accept	Nacalai Tesque	Cat#09277-56
Superdex 75 Increase 10/300 GL	cytiva	Cat#29148721
Deposited data
Antibody nucleotide sequence	This paper	GenBank accession number: MZ089617 to MZ089626
Structure of antibody (COVA2-04 or COVA2-39)-RBD complex	Wu et al., 2020b	PDB: 7JMO and 7JMP
Structure of 9-105-RBD complex	This paper	N/A
Experimental models: cell lines
293T	ATCC	CRL-3216
293A	Invitrogen	Cat#R70507
293FT/DSP1-7/ACE2/TMPRSS2	Yamamoto et al., 2020	N/A
293FT/DSP8-11/SARS-CoV-2-S	Yamamoto et al., 2020	N/A
Calu3-DSP1-7	Yamamoto et al., 2020	N/A
Calu-3	ATCC	HTB-55
Caco-2	ATCC	HTB-37
Vero	ATCC	CCL-81
ExpiCHO-S	GIBCO	Cat#A29127
Oligonucleotides
Primer: 3′ Cγ CH1: GGAAGGTGTGCACGCCGCTGGTC	Tiller et al., 2008	N/A
Primer: HcnestU: GG(ACTAGT)TCTTGTCCACCTTGGTGTTG	Coronella et al., 2000	N/A
Primer: P1-Cκ (modified): CAGCAGGCACACAACAGAGGCAGTTCC	He et al., 2014	N/A
Primer: 3′ Cλ: CACCAGTGTGGCCTTGTTGGCTTG	Tiller et al., 2008	N/A
Primer: Lnest: GCTCTAGAACTAATGCGTGACCTGGCAGCTGT	Coronella et al., 2000	N/A
Recombinant DNA
pIgGH	Ramirez Valdez et al., 2015	N/A
pKVA2	Ramirez Valdez et al., 2015	N/A
pLSH	Ramirez Valdez et al., 2015	N/A
SARS-CoV-2 Spike ORF expression plasmid	Sino Biological	Cat#VG40589-UT
pSARS-CoV-2-S-IRES-EGFP	This paper	N/A
psPAX2-IN/HiBiT	Ozono et al., 2020	N/A
pWPI-Luc2	Ozono et al., 2020	N/A
pC-SARS2-S-D614G	Ozono et al., 2021	N/A
pSARS-CoV-2-S-D614G-19del	This paper	N/A
SARS-CoV S-expressing plasmid	Sino Biological	Cat#VG40150-G-N
MERS-CoV S-expressing plasmid	Sino Biological	Cat#VG40069-G-N
Plasmids to express pSARS-CoV-2 S variants	This paper	N/A
Plasmids to express pSARS-CoV-2 S mutants	This paper	N/A
Software and algorithms
IMGT vquest	Brochet et al., 2008	http://imgt.org/
PyIR	Soto et al., 2020	https://github.com/crowelab/PyIR
FlowJo	TreeStar	Version 10.7.1 https://www.flowjo.com
BIAevaluation	GE healthcare	Version 4.1 http://www.cytivalifesciences.com/country-selection?originalItemPath=%2f
Prism	GraphPad Software	Version 8.4.3 https://www.graphpad.com/scientific-software/prism/