REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-ACE2 antibody	Abcam	Cat# ab15348
Goat Anti-Rabbit IgG H&L (HRP)	Abcam	Cat# ab6721
Anti-beta actin antibody [mAbcam 8226]	Abcam	Cat# ab8226
Anti-Mouse IgG H&L antibody	Abcam	Cat# ab205719
Bacterial and virus strains
SARS-CoV-2: pre-alpha type, D614G, B-1 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603286
SARS-CoV-2: gamma variant, TY7-501 strain	National Institute of Infectious Diseases	GISAID ID : EPI_ISL_833366
SARS-CoV-2: delta variant, BK325 strain	Research Foundation for Microbial Diseases of Osaka University	N/A
SARS-CoV-2: omicron variant, TY38-873 strain	National Institute of Infectious Diseases	GISAID ID : EPI_ISL_7418017
JM109 competent cells	SMOBIO	Cat# CC0202
Chemicals, peptides, and recombinant proteins
5-Fluorouracil	FUJIFILM Wako	Cat# 068-01401
KOD One PCR Master Mix -Blue-	TOYOBO	Cat# KMM-201
PrimeSTAR GXL DNA polymerase	TaKaRa Bio	Cat# R050A
Lipofectamin LTX Reagent with PLUS™ Reagent	Invitrogen	Cat# 15338100
SeaPlaque Agarose	LONZA	Cat# 50100
TriReagent	Molecular Research Center	Cat# TR118
Dulbecco’s modified Eagle’s Medium (DMEM)	Sigma-Aldrich	Cat# D6429
Minimum Essential Medium Eagle (MEM)	Sigma-Aldrich	Cat# M4655
Dulbecco's phosphate-buffered saline (D-PBS)	Nacalai Tesque	Cat# 14249
Fetal bovine serum (FBS)	Sigma-Aldrich	Cat# F7524
Penicillin (100 U/mL), and streptomycin (0.1 mg/mL) (PS)	Gibco	Cat# 1154887
Puromycin	Gibco	Cat# A1113803
G418 Sulfate, Geneticin	Gibco	Cat# 10131027
Opti-MEM	Gibco	Cat# 31985062
XbaI	NEB	Cat# R0145
NotI	NEB	Cat# R0189
rCutSmart Buffer	NEB	Cat# B6004
Polyethylenimine "Max" (PEI “Max”)	Polysciences, Inc.	Cat# 24765
Canget signal solution I	TOYOBO	Cat# NKB-201
Canget signal solution II	TOYOBO	Cat# NKB-301
ECL Prime Western Blotting Detection Reagents	Cytiva	Cat# RPN2232
RIPA buffer	Thermo Scientific	Cat# 89900
proteinase inhibitor cocktail	Thermo Scientific	Cat# 78430
Plus Protein Dual Color Standards	BIO-RAD	Cat#1610374
EzApply	ATTO	Cat# AE-1430
EzRun buffer	ATTO	Cat#AE-1410
Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs	Bio-Rad Laboratories, Inc.	Cat# 1704156
10×TBS	Bio-Rad Laboratories, Inc.	Cat# 1706435
Tween-20 (polyoxyethylene sorbitan monolaurate)	Nacalai Tesque	Cat# 35624-15
PVDF blocking reagent	TOYOBO	Cat# NYPBR01
e-PAGEL HR gel	ATTO	Cat#EHR-R1020L
Critical commercial assays
QIAamp viral RNA mini kit	QIAGEN	Cat# 52904
SuperScript™ III First-Strand Synthesis System for RT-PCR	Invitrogen	Cat# 18080051
DNA Ligation Kit Ver.2.1	TaKaRa Bio	Cat# 6022
GenNext RamDA-seq Single Cell Kit	TOYOBO	Cat# RMD-101
Nextera XT DNA Library Prep Kit	Illumina	Cat# FC-131-1096
Nextera XT Index Kit v2	Illumina	Cat# FC-131
Deposited data
Viral genome sequence of B-1 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603286
Viral genome sequence of A50-18 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603287
Viral genome sequence of H50-11 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603288
Viral genome sequence of L50-33 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603289
Viral genome sequence of L50-40 strain	Hirotaka Ebina, Osaka University1	NCBI: LC603290
Experimental models: Cell lines
Green monkey: Vero cells	ATCC	Cat# CCL-81; RRID: CVCL_0059
Green monkey: Vero cells with constitutive expression of TMPRSS II, VeroE6-TMPRSS II cells	Japanese Collection of Research Bioresources Cell Bank	Cat# JCRB1819; RRID: CVCL_YQ49
Syrian hamster: BHK-21(C-13) cells	Japanese Collection of Research Bioresources Cell Bank	Cat# JCRB9020; RRID: CVCL_1915
Syrian hamster: BHK-21(C-13) cells with constitutive expression of hACE2, BHK-hACE2 cells	This paper	N/A
Human 293T cells LX-293	ATCC	CRL-3216
Oligonucleotides
hACE2-cloning-Fw (AAATCTAGACGA TGTCAAGCTCTTCCTGGCTCCT)	Hirotaka Ebina, Osaka University1	N/A
hACE2-cloning-Rv (TTTGCGGCC GCTAAAAGGAGGTCTGAACATC ATCAGTGTTTTG)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-F1-Fw (CTATATAAGCAG AGCTCGTTTAGTGAACCGT attaaaggtttataccttcccaggtaac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F1-Rv (cagattcaacttgcat ggcattgttagtagccttatttaaggctcctgc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F2-Fw (gcaggagccttaaataa ggctactaacaatgccatgcaagttgaatctg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F2-Rv (ggtaggattttccacta cttcttcagagactggttttagatcttcgcaggc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F3-Fw (gcctgcgaagatctaaaa ccagtctctgaagaagtagtggaaaatcctacc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F3-Rv (ggtgcacagcgcagcttct tcaaaagtactaaagg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F4-Fw (caccactaattcaaccta ttggtgctttggacatatcagcatctatagta gctggtgg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F4-Rv (gtttaaaaacgattg tgcatcagctgactg	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F5-Fw (cacagtctgtaccgtctgcgg tatgtggaaaggttatggctgtagttgtgatc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F5-Rv (gcggtgtgtacatagcct cataaaactcaggttcccaataccttgaagtg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F6-Fw (cacttcaaggtattggga acctgagttttatgaggctatgtacacaccgc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F6-Rv (catacaaactgccaccatca caaccaggcaagttaaggttagatagcactctag)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F7-Fw (ctagagtgctatctaacctt aacttgcctggttgtgatggtggcagtttgtatg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F7-Rv (ctagagactagtggcaataa aacaagaaaaacaaacattgttcgtttagttgttaac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F8-Fw (gttaacaactaaacgaacaa tgtttgtttttcttgttttattgccactagtctctag)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F8-Rv (gcagcaggatccacaagaa caacagcccttgagacaactacagcaactgg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F9-Fw (ccagttgctgtagttgtctca agggctgttgttcttgtggatcctgctgc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F9-Rv (caatctccattggttgctcttcatc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F10-Fw (gatgaagagcaaccaatggagattg)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-F10-Rv (GGAGATGCCATG CCGACCCtttttttttttttttttttttttttgtca ttctcctaag)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-Linker-Fw (cttaggagaatgacaaa aaaaaaaaa aaaaaaaaaaaaaGGGTCGG CATGGCATCTCC)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-Linker-Rv (gttacctgggaaggta taaacctttaatACGGTTCACTAAACGA GCTCTGCTTATATAG)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-TS-F6-Rv (catacaaactgccacta tcacaaccaggcaagttaaggttagatagcactctag)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-TS-F7-Fw (ctagagtgctatctaaccttaa cttgcctggttgtgatagtggcagtttgtatg)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-4052T-Fw (tatattgacattaatggca attttcatccagattctgcca)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-4052T-Rv (ttgccattaatgtcaatataa agtaacaagttttctgtga)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-18782T-Fw (tgattgatgttcaacaatgg gtttttacaggtaacctaca)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-18782T-Rv (ccattgttgaacatcaat cataaacggattatagacgtaa)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-19285A-Fw (aaccttaacttgcctggttg tgatagtggcagtttgtatg)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-19285A-Rv (caaccaggcaagttaaggt tagatagcactctagtgtcaa)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-19550T-Fw (tctcgatgcttataacatga tgatctcagttggctttagc)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-19550T-Rv (tcatgttataagcatcgagata caatctgtactcattagc)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-20857A-Fw (ctgtaccctataatatga gaattatacattttggtgctggttct)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-20857A-Rv (tctcatattatagggtacagc taatgttaatgtgtttaaa)	Hirotaka Ebina, Osaka University1	N/A
CoV-2-G2-Fw (cggcagtgaggacaatcagacaactac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-G2-Rv (ggcttagcataattagctatagtatcccaagggac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-G6-Fw (tgtagatgatatcgtaaaaacagatggtacac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-G6-Rv (aacgtgttatacacgtagcagactttagtggtac)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-G7-Fw (aaaggttcaacacatggttgttaaagctgc)	Yoshiharu Matsuura, Osaka University5	N/A
CoV-2-G7-Rv (cgtacactttgtttctgagagagggtc)	Yoshiharu Matsuura, Osaka University5	N/A
covid-dp-4655-4683r (ggcactttgagagatctcatataccgagc)	Yoshiharu Matsuura, Osaka University5	N/A
covid-dp-18160-18186f (gttgacatacctggcatacctaaggac)	Yoshiharu Matsuura, Osaka University5	N/A
covid-dp-19712-19738r (caacaccatcaacttttgtgtaaacag)	Yoshiharu Matsuura, Osaka University5	N/A
covid-dp-20470-20496f (gcgcaaacaggttcatctaagtgtgtg)	Yoshiharu Matsuura, Osaka University5	N/A
Recombinant DNA
PiggyBac cDNA Cloning and Expression Vector	System Biosciences	PB514B-2
transposase expression vector	System Biosciences	PB200A-1
Software and algorithms
CLC Genomics Workbench 21	QIAGEN	N/A
Other
ImageQuant LAS-500 system	Cytiva	N/A
MiSeq platform	Illumina	N/A