REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-human CD31 APC	Biolegend	Cat#303116; RRID:AB_187751
Anti-human CD45 APC	Biolegend	Cat#368512; RRID:AB_2566372
Anti-human EpCAM FITC	Biolegend	Cat#324204; RRID:AB_756078
Mouse anti-HTII-280 IgM	Terrace Biotech	Cat#TB-27AHT2-280; RRID:AB_2832931_
PE goat anti-mouse IgM	Thermo-Fisher	Cat#12-5790-81; RRID:AB_465939
Bacterial and virus strains
SARS-CoV-2 GR clade (B.1.1.119)	KCDC	GISAID Number: EPI_ISL_812963
SARS-CoV-2 Alpha variant (B.1.1.7)	KCDC	GISAID Number: EPI_ISL_738139
SARS-CoV-2 Delta variant (B.1.617.2)	KCDC	GISAID Number: EPI_ISL_2887353
SARS-CoV-2 Omicron variant (B.1.1.529)	KCDC	GISAID Number: EPI_ISL_6959993
Biological samples
Human lung tissue samples	This paper	N/A
Chemicals, peptides, and recombinant proteins
Collagenase/Dispase	Sigma-Aldrich	Cat#10269638001
Dispase II	Sigma-Aldrich	Cat#4942078001
DNase I	Sigma-Aldrich	Cat#D4527-10KU
RBC lysis solution	Roche	Cat#11814389001
Accutase	STEMCELL Technologies	Cat#07920
Modified Eagle Medium	Gibco	Cat#11935-046
HI FBS	Gibco	Cat#10082-147
Serum-free DMEM	Gibco	Cat#41966-029
FBS	Gibco	Cat#16000-044
Growth Factor Reduced Matrigel	CORNING	Cat#356231
Y-27632	Sigma-Aldrich	Cat#Y0503
Advanced DMEM/F12	Thermo-Fisher	Cat#12634010
B27 supplement	Thermo-Fisher	Cat#17504044
FGF 7	PEPROTECH	Cat#100-19
FGF 10	PEPROTECH	Cat#100-26
Noggin	PEPROTECH	Cat#120-10C
EGF	PEPROTECH	Cat#100-15
N-Acetylcysteine	Sigma-Aldrich	Cat#A9165
Nicotinamide	Sigma-Aldrich	Cat#N0636
SB431542	Calbiochem	Cat#616461
CHIR99021	TOCRIS	Cat#4423
Recombinant Human R-Spondin 1 protein	R&D Systems	Cat#4645-RS
HEPES	Gibco	Cat#15140-122
Penicillin/Streptomycin	Gibco	Cat#15630-080
Glutamax-I	Gibco	Cat#35050-061
Amphotericin B	Sigma-Aldrich	Cat#A2942
Gentamicin	Sigma-Aldrich	Cat#G1397
Recovery solution	Corning	Cat#354253
CellTracker Green CMFDA Dye	Thermo-Fisher	Cat#C2925
BSA solution	Sigma-Aldrich	Cat#A8412s
Recombinant RNAse Inhibitor	Takarabio	Cat#2313A
dNTP Set. 100 mM Solutions	Thermo-Fisher	Cat#R0181
RIGAKU REAGENTS PEG 8000, 50%(w/v)	Rigaku reagents	Cat#25322-68-3
Maxima H Minus Reverse Transcriptase	Thermo-Fisher	Cat#EP0753
GTP(Tris bufferered solution 100 mM)	Thermo-Fisher	Cat#R1461
KAPA HiFi Hotstart PCR Kit	Roche	Cat#KK2502
Triton™ X-100 solution 10%	Sigma-Aldrich	Cat#93443-100ML
Sodium Chloride (5M)	Invitrogen	Cat#AM9760G
Magnesium Chlrode (1M)	Invitrogen	Cat#AM9530G
NN-Dimethylformamide	Sigma-Aldrich	Cat#D4551
Tris-HCl pH 7.5(1M)	Tech & Innovation	Cat#BTH-9183-001L
Tris-HCl pH 8.3(1M)	Tech & Innovation	Cat#BTH-9175-001L
Phusion™ High-Fidelity DNA Polymerase	Thermo-Fisher	Cat#F-530S
Nextera XT DNA library prep kit	Illumina	Cat#20015963
Critical commercial assays
C-chip Neubauer improved	iNCYTO	Cat#DHC-01
QIAamp viral mini kit	Qiagen	Cat#52904
NEBNext ARTIC SARS-CoV-2 FS kit	NEB	Cat#E7658S
Smart aliquotor CE chip	iBioChip	Cat#H2-SACE-5PK
Deposited data
Single-cell bam files of infected alveolar cells aligned by BWA and RNA sequencing of viral variants stock	EGA	EGA: EGAS00001006730
All scripts for calculating fraction of each SARS-CoV-2 variant	Zenodo	Zenodo: https://doi.org/10.5281/zenodo.7275406
Additional metadata for analysis	Mendeley	Mendeley data: https://doi.org/10.17632/j26ht6sy3p.1
Experimental models: Cell lines
VeroE6 cell	Kim et al.21	RRID:CVCL_0059
Oligonucleotides
OligoT30VN /5Biosg/ACGAGCATCAGCAGCATACGAT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN	Hagemann-Jensen et al.20	IDT
TSO /5Biosg/AGAGACAGATTGCGCAATGNN NNNNNNrGrGrG	Hagemann-Jensen et al.20	IDT
Forward primer TCGTCGGCAGCGTCAGATGTGTATAAGA GACAGATTGCGCAA∗T∗G	Hagemann-Jensen et al.20	IDT
Reverse primer ACGAGCATCAGCAGCATAC∗G∗A	Hagemann-Jensen et al.20	IDT
Software and algorithms
FACSDiva software version (ver. 6.1.3)	BD Biosciences
R (ver. 4.0.3)	Comprehensive R Archive Network	https://cran.r-project.org
Python (ver. 2.7.16)	Python Software Foundation	https://www.python.org/
Samtools (ver. 1.9)	Li et al.26	http://www.htslib.org; RRID:SCR_002105
Varscan2 (ver. 2.4.2)	Koboldt et al.27	http://dkoboldt.github.io/varscan/; RRID:SCR_006849
HaplotypeCaller	Poplin et al.28	https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller RRID:SCR_001876
Integrated Genomics Viewer	Thorvaldsdóttir et al.29	http://software.broadinstitute.org/software/igv/ RRID:SCR_011793
STAR (ver. 2.6.4)	Dobin et al.30	https://github.com/alexdobin/STAR;RRID:SCR_015899 RRID:SCR_004463
zUMIs	Parekh1 et al.31	https://github.com/sdparekh/zUMIs RRID:SCR_016139
BWA-MEM	Li32	http://bio-bwa.sourceforge.net/bwa.shtml RRID:SCR_010910
iVar	Grubaugh et al.33	https://github.com/andersen-lab/ivar
Fastp	Chen et al.34	https://github.com/OpenGene/fastp RRID:SCR_016962
Kraken	Wood et al.35	https://github.com/DerrickWood/kraken
Seurat	Stuart et al.36	https://github.com/satijalab/seurat RRID:SCR_007322
Scran	Lun et al.37	https://github.com/elswob/SCRAN RRID:SCR_016944
Scanpy	Wolf et al.38	https://github.com/scverse/scanpy RRID:SCR_018139
Gggenes		https://github.com/wilkox/gggenes