REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-SARS-CoV-2 S S1/S2 polyclonal antibody	Thermo Fisher Scientific	Cat# PA5-112048; RRID: AB_2866784
Normal rabbit IgG	SouthernBiotech	Cat# 0111-01; RRID: AB_2732899
APC-conjugated goat anti-rabbit IgG polyclonal antibody	Jackson ImmunoResearch	Cat# 111-136-144; RRID: AB_2337987
Mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111)	R&D systems	Cat# MAB10474-SP; RRID: N/A
Bacterial and virus strains
Recombinant SARS-CoV-2, rBA.2	Yamasoba et al., 2022b	N/A
Recombinant SARS-CoV-2, rBA.2.11	This study	N/A
Recombinant SARS-CoV-2, rBA.2.12.1	This study	N/A
Recombinant SARS-CoV-2, rBA.4/5	This study	N/A
Biological samples
Human sera	This study	N/A
Human airway epithelial cells derived from human induced pluripotent stem cells (iPSCs)	Yamamoto et al., 2017	N/A
Chemicals, peptides, and recombinant proteins
TransIT-LT1	Takara	Cat# MIR2300
Recombinant RNase inhibitor	Takara	Cat# 2313B
Carboxymethyl cellulose	Wako	Cat# 039-01335
4% Paraformaldehyde in PBS	Nacalai Tesque	Cat# 09154-85
Methylene blue	Nacalai Tesque	Cat# 22412-14
Fetal bovine serum	Sigma-Aldrich	Cat# 172012-500ML
Penicillin-streptomycin	Sigma-Aldrich	Cat# P4333-100ML
DMEM (high glucose)	Sigma-Aldrich	Cat# 6429-500ML
DMEM (low glucose)	Wako	Cat# 041-29775
EMEM	Sigma-Aldrich	Cat# M4655-500ML
EMEM	Wako	Cat# 056-08385
Expi293 expression medium	Thermo Fisher Scientific	Cat# A1435101
PneumaCult ALI medium	STEMCELL Technologies	Cat# ST-05001
Heparin	Nacalai Tesque	Cat# 17513-96
Y-27632	LC Laboratories	Cat# Y-5301
Hydrocortisone	Sigma-Aldrich	Cat# H0135
Puromycin	InvivoGen	Cat# ant-pr-1
Hygromycin	Nacalai Tesque	Cat# 09287-84
Blasticidin	InvivoGen	Cat# ant-bl-1
G418	Nacalai Tesque	Cat# G8168-10ML
KpnI	New England Biolab	Cat# R0142S
NotI	New England Biolab	Cat# R1089S
PEI Max	Polysciences	Cat# 24765-1
Doxycycline	Takara	Cat# 1311N
TURBO DNase	Thermo Fisher Scientific	Cat# AM2238
Opti-MEM	Thermo Fisher Scientific	Cat# 11058021
Triton X-100	Nacalai Tesque	Cat# 35501-15
Recombinant RNase inhibitor	Takara	Cat# 2313B
Poly-L-lysine	Sigma	Cat# P4832
Hoechst 33342	Thermo Fisher Scientific	Cat# H3570
Fluoromount-G	SouthernBiotech	Cat# 0100-01
EnduRen live cell substrate	Promega	Cat# E6481
AddaVax	InvivoGen	Cat# vac-adx-10
Polyethylene glycol 6000	Hampton Research	Cat# HR2-533
2-methyl-2,4-pentanediol	Hampton Research	Cat# HR2-627
MES	Nacalai Tesque	Cat# 21623-26
Glycerol	Nacalai Tesque	Cat# 17018-25
Dexamethasone	Sigma-Aldrich	Cat# D4902
KGF	PeproTech	Cat# 100-19
8-Br-cAMP	Biolog	Cat# B007
3-Isobutyl 1-methylxanthine (IBMX)	FUJIFILM Wako	Cat# 095-03413
CHIR99021	Axon Medchem	Cat# 1386
SB431542	Wako	Cat# 198-16543
Soluble human ACE2 (residues 18-740)	Yamasoba et al., 2022b	N/A
SARS-CoV-2 B.1.1 RBD	Kimura et al., 2022a; Motozono et al., 2021	N/A
SARS-CoV-2 BA.1 RBD	Dejnirattisai et al., 2022	N/A
SARS-CoV-2 BA.2 RBD	Yamasoba et al., 2022b	N/A
SARS-CoV-2 BA.4/5 RBD	This study	N/A
Bilirubin	Sigma-Aldrich	Cat# 14370-1G
Medetomidine hydrochloride (Domitor®)	Nippon Zenyaku Kogyo	N/A
Midazolam	FUJIFILM Wako Chemicals	Cat# 135-13791
Butorphanol (Vetorphale®)	Meiji Seika Pharma	N/A
Alphaxaone (Alfaxan®)	Jurox	N/A
Isoflurane	Sumitomo Dainippon Pharma	N/A
EnVision FLEX target retrieval solution high pH	Agilent	Cat# K8004
Critical commercial assays
QIAamp viral RNA mini kit	Qiagen	Cat# 52906
NEB next ultra RNA library prep kit for Illumina	New England Biolabs	Cat# E7530
MiSeq reagent kit v3	Illumina	Cat# MS-102-3001
One Step TB Green PrimeScript PLUS RT-PCR kit	Takara	Cat# RR096A
SARS-CoV-2 direct detection RT-qPCR kit	Takara	Cat# RC300A
L452R (SARS-CoV-2) primer/probe set v2	Takara	Cat# RC346A
E484A (SARS-CoV-2) primer/probe set v2	Takara	Cat# RC322A
Nano Glo HiBiT lytic detection system	Promega	Cat# N3040
KAPA HiFi HotStart ReadyMix kit	Roche	Cat# KK2601
PrimeSTAR GXL DNA polymerase	Takara	Cat# R050A
Bright-Glo luciferase assay system	Promega	Cat# E2620
One-Glo luciferase assay system	Promega	Cat# E6130
Deposited data
Viral genome sequencing data of working viral stocks (see also Table S7)	This paper	SRA: DRR378901–DRR378909 (https://www.ncbi.nlm.nih.gov/sra)
Structure of the BA.4/5 S RBD-human ACE2 complex	This study	PDB: 7XWA
Experimental models: Cell lines
Human: HEK293T cells	ATCC	CRL-3216
Human: HEK293 cells	ATCC	CRL-1573
Human: HEK293-ACE2 cells	Motozono et al., 2021	N/A
Human: HEK293-ACE2/TMPRSS2 cells	Motozono et al., 2021	N/A
Human: HEK293-C34 cells	Torii et al., 2021	N/A
Human: HEK293S GnTI(-) cells	Reeves et al., 2002	N/A
Human: Expi293F cells	Thermo Fisher Scientific	Cat# A14527
Human: HOS-ACE2/TMPRSS2 cells	Ferreira et al., 2021; Ozono et al., 2021	N/A
Human: Calu-3/DSP1-7 cells	Yamamoto et al., 2020	N/A
African green monkey (Chlorocebus sabaeus): Vero cells	JCRB Cell Bank	JCRB0111
African green monkey (Chlorocebus sabaeus): VeroE6/TMPRSS2 cells	JCRB Cell Bank	JCRB1819
Yeast (Saccharomyces cerevisiae): strain EBY100	ATCC	MYA-4941
Experimental models: Organisms/strains
BALB/cCrSlc mice (female, 7 weeks old)	Japan SLC Inc.	http://www.jslc.co.jp/pdf/mouse/2020/004_BALB_cCrClc.pdf
Slc:Syrian hamsters (male, 4 weeks old)	Japan SLC Inc.	http://www.jslc.co.jp/pdf/hamster/2020/028_Slc_Syrian.pdf
Oligonucleotides
Omi_ins214s-F1: TTC TAA GCA CAC GCC TAT TAT AGT GC	Yamasoba et al., 2022b	N/A
Omi_ins214s-R1: TAA AGC CGA AAA ACC CTG AGG	Yamasoba et al., 2022c	N/A
Omi_ins214s: FAM-TGA GCC AGA AGA TC-MGB	Yamasoba et al., 2022b	N/A
Primers for the construction of plasmids expressing the codon-optimized S proteins of L452R/Q/M-bearing variants, see Table S6	This study	N/A
Primers for SARS-CoV-2 reverse genetics, see Table S6	This study	N/A
RT-qPCR, forward: AGC CTC TTC TCG TTC CTC ATC AC	Kimura et al., 2022b; Meng et al., 2022; Motozono et al., 2021; Saito et al., 2022; Suzuki et al., 2022; Yamasoba et al., 2022b	N/A
RT-qPCR, reverse: CCG CCA TTG CCA GCC ATT C	Kimura et al., 2022b; Meng et al., 2022; Motozono et al., 2021; Saito et al., 2022; Suzuki et al., 2022; Yamasoba et al., 2022b	N/A
Primers for the construction of yeast-optimized SARS-CoV-2 BA.2 RBD expression plasmid, see Table S6	This study	N/A
Recombinant DNA
Plasmid: pCAGGS	Niwa et al., 1991	N/A
Plasmid: psPAX2-IN/HiBiT	Ozono et al., 2020	N/A
Plasmid: pWPI-Luc2	Ozono et al., 2020	N/A
Plasmid: pJYDC1	Addgene	Cat# 162458
Plasmid: pHLsec	Aricescu et al., 2006	N/A
Plasmid: pDSP1-7	Kondo et al., 2011	N/A
Plasmid: pDSP8-11	Kondo et al., 2011	N/A
Plasmid: pCAGGS	Niwa et al., 1991	N/A
Plasmid: pC-B.1.1 S	Motozono et al., 2021; Ozono et al., 2021	N/A
Plasmid: pC-BA.2 S	Yamasoba et al., 2022b	N/A
Plasmid: pC-BA.2.9.1 S	This study	N/A
Plasmid: pC-BA.2.11 S	This study	N/A
Plasmid: pC-BA.2.12.1 S	This study	N/A
Plasmid: pC-BA.4/5 S	This study	N/A
Plasmid: pC-BA.2 L452Q S	This study	N/A
Plasmid: pC-BA.2 S704L S	This study	N/A
Plasmid: pC-BA.2 HV69-70del S	This study	N/A
Plasmid: pC-BA.2 F486V S	This study	N/A
Plasmid: pC-BA.2 R493Q S	This study	N/A
Software and algorithms
fastp v0.21.0	Chen et al., 2018	https://github.com/OpenGene/fastp
BWA-MEM v0.7.17	Li and Durbin, 2009	http://bio-bwa.sourceforge.net
SAMtools v1.9	Li et al., 2009	http://www.htslib.org
snpEff v5.0e	Cingolani et al., 2012	http://pcingola.github.io/SnpEff
roblanf/sarscov2phylo: 13-11-20 (GISAID phylogenetic analysis pipeline)	GitHub	https://github.com/roblanf/sarscov2phylo
Minimap2 v2.17	Li, 2018	https://github.com/lh3/minimap2
trimAl v1.2	Capella-Gutiérrez et al., 2009	http://trimal.cgenomics.org
RAxML v8.2.12	Stamatakis, 2014	https://cme.h-its.org/exelixis/web/software/raxml
CmdStan v2.28.1	The Stan Development Team	https://mc-stan.org
CmdStanr v0.4.0	The Stan Development Team	https://mc-stan.org/cmdstanr/
R v4.1.3	The R Foundation	https://www.r-project.org/
Sequencher v5.1 software	Gene Codes Corporation	N/A
In-house scripts	This study	https://github.com/TheSatoLab/BA.2_related_Omicrons
Prism 9 software v9.1.1	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
Fiji software v2.2.0	ImageJ	https://fiji.sc
FlowJo software v10.7.1	BD Biosciences	https://www.flowjo.com/solutions/flowjo
Python v3.7	Python Software Foundation	https://www.python.org
FinePointe Station and Review softwares v2.9.2.12849	STARR	https://www.datasci.com/products/software/finepointe-software
NDP.scan software v3.2.4	Hamamatsu Photonics	https://nanozoomer.hamamatsu.com/jp/en/why_nanozoomer/scan.html
PyMOL	Schrödinger	https://pymol.org/2/
XDS	Kabsch, 2010	https://xds.mr.mpg.de/
BUSTER v2.10.4	Global Phasing Ltd.	https://www.globalphasing.com/
MolProbity	Duke Biochemistry	http://molprobity.biochem.duke.edu/index.php
COOT	Emsley and Cowtan, 2004	http://www.mrc-lmb.cam.ac.uk/personal/peemsley/coot/
Phaser	McCoy et al., 2007	https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software
Phenix	Adams et al., 2010	http://www.phenix-online.org/
Other
Centro XS3 LB960	Berthhold Technologies	N/A
GloMax explorer multimode microplate reader 3500	Promega	N/A
FACS Canto II	BD Biosciences	N/A
GISAID database	Khare et al., 2021	https://www.gisaid.org/
BD microtainer blood collection tubes	BD Biosciences	Cat# 365967
24-well Cell Culture Insert	Falcon	Cat# 353104
cOmplete His-Tag Purification Resin	Roche	Cat# 05 893 682 001
Superdex 75 increase 10/300	Cytiva	Cat# 29148721
3,3’-diaminobenzidine tetrahydrochloride	Dako	Cat# DM827
MAS-GP-coated glass slides	Matsunami Glass	Cat# S9901
A1Rsi Confocal Microscope	Nikon	N/A
QuantStudio 3 Real-Time PCR system	Thermo Fisher Scientific	N/A
CFX Connect Real-Time PCR Detection system	Bio-Rad	N/A
Eco Real-Time PCR System	Illumina	N/A
qTOWER3 G Real-Time System	Analytik Jena	N/A
7500 Real-Time PCR System	Thermo Fisher Scientific	N/A
Autostainer Link 48	Dako	N/A