REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
FITC-conjugated anti-human CD3 antibody	Biolegend	Cat# 300440; RRID: AB_2562046
BV510-conjugated anti-human CD3 antibody	Biolegend	Cat# 317331; RRID: AB_2561376
APC-Cy7-conjugated anti-human CD8 antibody	Biolegend	Cat# 301016; RRID: AB_314134
PerCP-Cy5.5-conjugated anti-human CD14 antibody	Biolegend	Cat# 325622; RRID: AB_893250
PerCP-Cy5.5-conjugated anti-human CD19 antibody	Biolegend	Cat# 302230; RRID: AB_2073119
PE-Cy7-conjugated anti-human CD25 antibody	Biolegend	Cat# 356107; RRID: AB_2561974
APC-conjugated anti-human CD137 antibody	Biolegend	Cat# 309809; RRID: AB_830671
BV421-conjugated anti-human CD107a antibody	Biolegend	Cat# 328625; RRID: AB_10899581
PE-conjugated anti-human IFN-γ antibody	BD Biosciences	Cat# 554552; RRID: AB_395474
PE-Cy7-conjugated anti-human TNF-α antibody	Biolegend	Cat# 502930; RRID: AB_2204079
APC-conjugated anti-human IL-2 antibody	Biolegend	Cat# 500310; RRID: AB_315097
Anti-ACE2 antibody	R&D Systems	Cat# AF933; RRID: AB_355722
APC-conjugated anti-goat IgG	R&D Systems	Cat# F0108; RRID: AB_573124
Goat normal IgG	R&D Systems	Cat# AB-108-C; RRID: AB_354267
Anti-SARS-CoV-2 S antibody	GeneTex	Cat# GTX635654; RRID: AB_2888548
APC-conjugated anti-rabbit IgG	Jackson ImmunoResearch	Cat# 111-136-144; RRID: AB_2337987
Rabbit normal IgG	SouthernBiotech	Cat# 0111-01; RRID: AB_2732899
Bacterial and virus strains
SARS-CoV-2 (strain WK-521)	Matsuyama et al., 2020	GISAID ID: EPI_ISL_408667
Biological samples
Human PBMCs	This study	N/A
Chemicals, peptides, and recombinant proteins
Ficoll-Paque Plus	GE Healthcare Life Sciences	Cat# 17-1440-03
RPMI1640 medium	Thermo Fisher Scientific	Cat# 11875101
Fetal calf serum (FCS)	Sigma-Aldrich	Cat# 172012-500ML
Penicillin streptomycin (PS)	Sigma-Aldrich	Cat# P4333-100ML
Dulbecco’s modified Eagle’s medium (high glucose)	Wako	Cat# 044-29765
Eagle’s minimum essential medium (with L-glutamine and phenol red)	Wako	Cat# 051-07615
Dulbecco’s modified Eagle’s medium (low glucose)	Wako	Cat# 041-29775
G418	Nacalai Tesque	Cat# G8168-10ML
Dulbecco’s modified Eagle’s medium (high glucose)	Sigma-Aldrich	Cat# R8758-500ML
Blasticidin	InvivoGen	Cat# ant-bl-1
Ham’s F-12K medium	Wako	Cat# 080-08565
Expi293 expression medium	Thermo Fisher Scientific	Cat# A1435101
SARS-CoV-2 PepTivator peptide pools	Miltenyi Biotec	Cat# 130-126-700
Recombinant human IL-2	Peprotec	Cat# 200-02
NF9 peptide (NYNYLYRLF, residues 448-456 of the SARS-CoV-2 S protein)	This study	N/A
L452R peptide (NYNYRYRLF, L5R in NF9)	This study	N/A
Y453F peptide (NYNYLFRLF, Y6F in NF9)	This study	N/A
7-aminoactinomycin D	Biolegend	Cat# 420404
Paraformaldehyde	Nacalai Tesque	Cat# 09154-85
Brefeldin A	Sigma-Aldrich	Cat# B7651
Monensin	Biolegend	Cat# 420701
PrimeSTAR GXL DNA polymerase	Takara	Cat# R050A
KpnI	New England Biolab	Cat# R0142S
NotI	New England Biolab	Cat# R1089S
MluI-HF	New England Biolab	Cat# R3198L
SmaI	New England Biolab	Cat# R0141L
HpaI	New England Biolab	Cat# R0105L
XhoI	New England Biolab	Cat# R0146S
Bilirubin	Sigma-Aldrich	Cat# 14370-1G
CF640R succinimidyl ester	Biotium	Cat# 92108
Lipofectamine 3000	Thermo Fisher Scientific	Cat# L3000015
Lipofectamine 2000	Thermo Fisher Scientific	Cat# 11668019
DNase I	Sigma-Aldrich	Cat# 11284932001
TransIT-LT1	Takara	Cat# MIR2300
Puromycin	InvivoGen	Cat# ant-pr-1
Doxycycline	Takara	Cat# 1311N
TURBO DNase	Thermo Fisher Scientific	Cat# AM2238
Minimum essential medium (2 × ), no phenol red	Thermo Fisher Scientific	Cat# 11935046
Nonessential amino acid	Thermo Fisher Scientifc	Cat# 11140-050
Carboxymethyl cellulose	Sigma-Aldrich	Cat# C9481-500G
Formaldehyde	Nacalai Tesque	Cat# 37152-51
Crystal violet	Nacalai Tesque	Cat# 09804-52
Methylene blue	Nacalai Tesque	Cat# 22412-14
Recombinant RNase inhibitor	Takara	Cat# 2313B
Transcriptor reverse transcriptase	Roche	Cat# 03531317001
Critical commercial assays
Cytofix/Cytoperm Fixation/Permeabilization solution kit	BD Biosciences	Cat# 554714
QIAamp RNA blood mini kit	QIAGEN	Cat# 52304
SuperScript III reverse transcriptase	Thermo Fisher Scientific	Cat# 18080085
ExpiFectamine 293 transfection kit	Thermo Fisher Scientific	Cat# A14525
KAPA HiFi HotStart ReadyMix kit	Roche	Cat# KK2601
One-Glo luciferase assay system	Promega	Cat# E6130
GENEART site-directed mutagenesis system	Thermo Fisher Scientific	Cat# A13312
QIAamp viral RNA mini kit	QIAGEN	Cat# 52906
One Step TB Green PrimeScript PLUS RT-PCR kit	Takara	Cat# RR096A
SARS-CoV-2 direct detection RT-qPCR kit	Takara	Cat# RC300A
GeneJET gel extraction kit	Thermo Fisher Scientific	Cat# K0692
EnduRen live cell substrate	Promega	Cat# E6481
Experimental models: Cell lines
Human: C1R-A2402 cells	Karaki et al., 1993	N/A
Human: HEK293 cells	ATCC	CRL-1573
Human: HEK293T cells	ATCC	CRL-3216
African green monkey (Chlorocebus sabaeus): Vero cells	JCRB	JCRB0111
African green monkey (Chlorocebus sabaeus): VeroE6/TMPRSS2 cells	JCRB	JCRB1819
Mink (Neovison vison): Mv.1.Lu cells	ATCC	CCL-64
Human: HEK293-C34 cells	Torii et al., 2021	N/A
Human: HEK293-ACE2 cells	This study	N/A
Human: A549-ACE2 cells	This study	N/A
Human: Expi293F cells	Thermo Fisher Scientific	Cat# A14527
Yeast (Saccharomyces cerevisiae): strain EBY100	ATCC	MYA-4941
Oligonucleotides
Forward primer for pC-SARS2-S: TTG GGTACC ATG TTT GTG TTC CTG GTG CTG	Ozono et al., 2021	N/A
Reverse primer for pC-SARS2-S: GTG GCGGCCGC TCT AGA TTC AGG TGT AGT GCA GTT T	Ozono et al., 2021	N/A
Forward primer for S L452R: GTG GGA GGC AAC TAC AAC TAC CGT TAC	This study	N/A
Forward primer for S Y453F: GTG GGA GGC AAC TAC AAC TAC CTC TTC AGA	This study	N/A
Reverse primer for S L452R/L453F: GTT GTA GTT GCC TCC CAC CTT	This study	N/A
Forward primer for S N501Y: TCC TAT GGC TTC CAA CCA ACC TAT GGA	This study	N/A
Reverse primer for S N501Y: TGG TTG GAA GCC ATA GGA TTG	This study	N/A
Forward primer for S S13I: TGC CAC TGG TGT CCA TCC AGT GTG TGA ACC T	This study	N/A
Reverse primer for S S13I: AGG TTC ACA CAC TGG ATG GAC ACC AGT GGC A	This study	N/A
Forward primer for S W152C: GAA CAA CAA GTC CTG TAT GGA GTC TGA GTT C	This study	N/A
Reverse primer for S W152C: GAA CTC AGA CTC CAT ACA GGA CTT GTT GTT C	This study	N/A
Forward primer for S D614G: CTG TGC TCT ACC AGG GTG TGA ACT GTA CTG A	This study	N/A
Reverse primer for S D614G: TCA GTA CAG TTC ACA CCC TGG TAG AGC ACA G	This study	N/A
Forward primer for S HV69-70del: GGT TCC ATG CCA TCT CTG GCA CCA ATG GCA	This study	N/A
Reverse primer for S HV69-70del: TGC CAT TGG TGC CAG AGA TGG CAT GGA ACC	This study	N/A
Mink ACE2 forward primer for cloning: ATG TTA GGC TCT TCC TGG CTC CTT	This study	N/A
Mink ACE2 reverse primer for cloning: CTA AAA TGA CGT CTG AAC ATC ATC GAC	This study	N/A
Mink ACE2 forward primer for the preparation of mink ACE2 expression: TTG GGT ACC ATG TTA GGC TCT TCC TGG CTC C	This study	N/A
Mink ACE2 reverse primer for the preparation of mink ACE2 expression: AAA GAT CTC GAG CTA AAA TGA CGT CTG AAC ATC	This study	N/A
Primer for the preparation of RBD L452R expression plasmid (RBD L452R):GGA CAG CAA GGT GGG AGG CAA CTA CAA CTA CAG ATA CAG ACT GTT CAG GAA GAG CAA C	This study	N/A
Primer for the preparation of RBD Y453F expression plasmid (RBD Y453F): CTC AAA TGG TTT CAG GTT GCT CTT CCT GAA CAG TCT GAA GAG GTA GTT GTA GTT GCC TCC C	This study	N/A
Primer for the preparation of RBD N501Y expression plasmid (RBD N501Y): GTA TGG TTG GTA GCC CAC TCC ATA GGT TGG TTG GAA GCC ATA GGA TTG	This study	N/A
Primer for the preparation of the RBD expression plasmid CAT GGG AAA ACA TGT TGT TTA CGG AG	This study	N/A
Primer for the preparation of the RBD expression plasmid preparation: GCA GCC CCA TAA ACA CAC AGT AT	This study	N/A
Forward primer for the preparation of Fragment 8, S L452R: CTA AGG TTG GTG GTA ATT ATA ATT ACC GGT ATA GAT TGT TTA GGA AGT CTA ATC	This study	N/A
Reverse primer for the preparation of Fragment 8, S L452R: GAT TAG ACT TCC TAA ACA ATC TAT ACC GGT AAT TAT AAT TAC CAC CAA CCT TAG	This study	N/A
Forward primer for the preparation of Fragment 8, S Y453F: GGT TGG TGG TAA TTA TAA TTA CCT GTT TAG ATT GTT TAG GAA GTC TAA TCT C	This study	N/A
Reverse primer for the preparation of Fragment 8, S Y453F: GAG ATT AGA CTT CCT AAA CAA TCT AAA CAG GTA ATT ATA ATT ACC ACC AAC C	This study	N/A
Forward primer for the preparation of Fragment 8, S N501Y: CAA TCA TAT GGT TTC CAA CCC ACT TAT GGT GTT GGT TAC CAA CCA TAC AG	This study	N/A
Reverse primer for the preparation of Fragment 8, S N501Y: CTG TAT GGT TGG TAA CCA ACA CCA TAA GTG GGT TGG AAA CCA TAT GAT TG	This study	N/A
SARS-CoV-2 S forward primer for the mutation verification (WK-521, 22607-22630 forward): GCA TCT GTT TAT GCT TGG AAC AGG	Torii et al., 2021	N/A
SARS-CoV-2 S reverse primer for the mutation verification (WK-521, 23342-23367 reverse): CCT GGT GTT ATA ACA CTG ACA CCA CC	Torii et al., 2021	N/A
SARS-CoV-2 N forward primer for real-time RT-PCR: AGC CTC TTC TCG TTC CTC ATC AC	This study	N/A
SARS-CoV-2 N reverse primer for real-time RT-PCR: CCG CCA TTG CCA GCC ATT C	This study	N/A
Forward primer for competition assay: CAG GGC AAA CTG GAA AGA TT	This study	N/A
Reverse primer for competition assay: TCA GCA ATG TCT CTG CCA AA	This study	N/A
Sequencing primer for competition assay: CAG GGC AAA CTG GAA AGA TT	This study	N/A
Random hexamer	Sigma-Aldrich	N/A
Recombinant DNA
Plasmid: pC-SARS2-S	Ozono et al., 2021	N/A
Plasmid: pCAGGS	Niwa et al., 1991	N/A
Plasmid: pC-SARS2-S-L452R	This study	N/A
Plasmid: pC-SARS2-S-Y453F	This study	N/A
Plasmid: pC-SARS2-S-N501Y	This study	N/A
Plasmid: pC-SARS2-S-D614G	Ozono et al., 2021	N/A
Plasmid: pC-SARS2-S-B.1.429 [S13I/W152C/L452R/D614G]	This study	N/A
Plasmid: pC-SARS2-S-B.1.1.298 [HV69-70del/Y453F/D614G]	This study	N/A
Plasmid: pTargeT-human ACE2	Fukushi et al., 2007	N/A
Plasmid: pLV-EF1a-IRES-Puro	Addgene	Cat# #85132
Plasmid: pLV-EF1a-human ACE2-IRES-Puro	This study	N/A
Plasmid: pC-ACE2	Ozono et al., 2021	N/A
Plasmid: pC-mink ACE2	This study	N/A
Plasmid: pHL-sec	Addgene	Cat# 99845
Plasmid: pHL-sec-human ACE2 (residues 18-740)	Zahradník et al., 2021a	N/A
Plasmid: pJYDC1	Addgene	Cat# 162458
Plasmid: pJYDC1-SARS-CoV-2 S RBD (residues 336-528)	Zahradník et al., 2021a	N/A
Plasmid: pJYDC1-SARS-CoV-2 S RBD L452R	This study	N/A
Plasmid: pJYDC1-SARS-CoV-2 S RBD Y453F	This study	N/A
Plasmid: pJYDC1-SARS-CoV-2 S RBD N501Y	This study	N/A
Plasmid: psPAX2-IN/HiBiT	Ozono et al., 2020	N/A
Plasmid: pWPI-Luc2	Ozono et al., 2020	N/A
Plasmid: pC-TMPRSS2	Ozono et al., 2021	N/A
Plasmid: pΔ-NRF	Naldini et al., 1996	N/A
Plasmid: pVSV-G	Addgene	Cat# 138479
Plasmid: template plasmids for the preparation of the partial SARS-CoV-2 genome fragments for CPER, see Table S6	Torii et al., 2021	N/A
Plasmid: pDSP1-7	Kondo et al., 2011	N/A
Plasmid: pDSP8-11	Kondo et al., 2011	N/A
Software and algorithms
NetMHCpan (v 4.1)	Reynisson et al., 2020; Katoh and Standley, 2013	http://www.cbs.dtu.dk/services/NetMHCpan/
NetMHC (v 4.0)	Andreatta and Nielsen, 2016; Lundegaard et al., 2008; Nielsen et al., 2003	http://www.cbs.dtu.dk/services/NetMHC/
SMM tool	Andreatta and Nielsen, 2016	http://tools.iedb.org/mhci/help/
PickPocket (v 1.1)	Zhang et al., 2009	http://www.cbs.dtu.dk/services/PickPocket/
NetMHCcons (v 1.1)	Karosiene et al., 2012	http://www.cbs.dtu.dk/services/NetMHCcons/
MAFFT suite (v7.467)	Katoh and Standley, 2013	https://mafft.cbrc.jp/alignment/software/
ModelTest-NG (v0.1.5)	Darriba et al., 2020	https://github.com/ddarriba/modeltest
RAxML-NG (v1.0.0)	(Kozlov et al., 2019)	https://github.com/amkozlov/raxml-ng
FigTree (v1.4.4)	Andrew Rambaut	http://tree.bio.ed.ac.uk/software/figtree
trimAl (v1.4.rev22)	Capella-Gutiérrez et al., 2009	http://trimal.cgenomics.org
Python (v3.7)	Python Software Foundation	https://www.python.org
Sequencher (v5.1)	Gene Codes Corporation	N/A
PyMOL (v2.3.0)	Schrödinger	https://pymol.org/2/
UCSF Chimera (v1.13)	Pettersen et al., 2004	N/A
Prism	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
Tracy	Rausch et al., 2020	https://www.gear-genomics.com/teal/
EditR	Kluesner et al., 2018	http://baseeditr.com
Other
GISAID	Freunde von GISAID e.V.	https://www.gisaid.org
Pangolin	Rambaut et al., 2020	https://cov-lineages.org/pangolin.html
0.45-μm pore size filter	Thermo Fisher Scientific	Cat# 09-740-114
40-μm cell strainer	SPL Life Sciences	Cat# 93040
HisTrap Fast Flow column	Cytiva	Cat# 17-5255-01
Ultracel-3 regenerated cellulose membrane	Merck	Cat# UFC900324
0.45-μm pore size filter	Merck	Cat# SLGVR33RB
96-well black plate	PerkinElmer	Cat# 6005225