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 Scientific	Cat#12-5790-81; RRID:AB_465939
Rabbit pro-SFTPC	Merck Millipore	Cat#Ab3786; RRID:AB_92588
DAPI	Sigma-Aldrich	Cat#D9543
Alexa Fluor 647 Phalloidin	Thermo Fisher Scientific	Cat#A22287; RRID:AB_2620155
CRB3 Antibody	NOVUS BIOLOGICALS	Cat#NBP1-81186; RRID:AB_11038157
Rabbit anti-SCRIB	GeneTex	Cat#GTX107692; RRID:AB_1241297
Goat RAGE/AGER antibody	R&D Systems	Cat#AF1145; RRID:AB_354628
Recombinant Anti-Aquaporin 5 antibody	abcam	Cat#ab92320; RRID:AB_2049171
Mouse anti-ABCA3	Seven Hills Bioreagents	Cat#WRAB-ABCA3; RRID:AB_577286
Rabbit anti-HOPX	Santa Cruz	Cat#sc-30216; RRID:AB_2120833
Rat anti-SCGB1A1	R&D SYSTEMS	Cat#MAB4218; RRID:AB_2183286
Rabbit anti-KRT5	Biolegend	Cat#905501; RRID:AB_2565050
Mouse anti-TP63	abcam	Cat#ab735; RRID:AB_305870
Anti-ACE2 antibody	abcam	Cat#ab15348; RRID:AB_301861
TMPRSS2 antibody (H-4)	Santa Cruz Biotechnology	Cat#515727
Anti-pro-surfactant Protein C	abcam	Cat#ab90716; RRID:AB_10674024
Anti-dsRNA IgM monoclonal antibody	SCICONS	Cat#10030005
SARS-CoV-2-Nucleocapsid antibody (NP)	Sino Biological	Cat#40143-MM05; RRID:AB_2827977
SARS-CoV Nucleoprotein antibody (NP)	Sino Biological	Cat#40143-T62
Human/Mouse E-Cadherin antibody	R&D SYSTEMS	Cat#AF748; RRID:AB_355568
MX1 antibody	GeneTex	Cat#GTX110256; RRID:AB_1950963
Alexa Fluor 488 AffiniPure Donkey Anti-Rabbit IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#711-545-152; RRID: AB_2313584
Alexa Fluor 594 AffiniPure Donkey Anti-Rabbit IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#711-585-152; RRID: AB_2340621
Alexa Fluor 647 AffiniPure Donkey Anti-Rabbit IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#711-605-152; RRID: AB_2492288
Alexa Fluor 488 AffiniPure Donkey Anti-Mouse IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#715-545-151; RRID: AB_2341099
Alexa Fluor 594 AffiniPure Donkey Anti-Mouse IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#715-585-151; RRID: AB_2340855
Alexa Fluor 647 AffiniPure Donkey Anti-Mouse IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#705-605-147; RRID: AB_2340437
Alexa Fluor 488 AffiniPure Donkey Anti-Goat IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#705-545-147; RRID: AB_2336933
Alexa Fluor 594 AffiniPure Donkey Anti-Goat IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#705-585-147; RRID: AB_2340433
Alexa Fluor 647 AffiniPure Donkey Anti-Goat IgG (H+L)	Jackson ImmunoResearch Laboratories	Cat#705-605-147; RRID: AB_2340437
Goat anti-Mouse IgM (heavy chain), Alexa Fluor 555	Thermo Fisher Scientific	Cat#A-21426; RRID:AB_2535847
Donkey anti-Rabbit IgG (H+L) Alexa Fluor 488	Thermo Fisher Scientific	Cat#A-21206; RRID:AB_2535792
Donkey anti-Rabbit IgG (H+L), Alexa Fluor 555	Thermo Fisher Scientific	Cat#A-31572; RRID:AB_162543
Donkey anti-Rabbit IgG (H+L), Alexa Fluor 647	Thermo Fisher Scientific	Cat#A-31573; RRID:AB_2536183
Donkey anti-Mouse IgG (H+L), Alexa Fluor 488	Thermo Fisher Scientific	Cat#A-21202; RRID:AB_141607
Donkey anti-Mouse IgG (H+L) Alexa Fluor 647	Thermo Fisher Scientific	Cat#A-31571; RRID:AB_162542
Donkey anti-Rat IgG (H+L), Alexa Fluor 488	Thermo Fisher Scientific	Cat#A-21208; RRID:AB_2535794
Bacterial and Virus Strains
SARS-CoV-2: BetaCov/Korea/KCDC03	Kim et al., 2020b	N/A
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
Crystal violet solution	Sigma-Aldrich	Cat#V5265
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
Human Serum	Sigma-Aldrich	Cat#H4522
Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix, LDEV-free	CORNING	Cat#354230
Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix, Phenol Red-free, LDEV-free	CORNING	Cat#356231
Y-27632	Sigma-Aldrich	Cat#Y0503
Advanced DMEM/F12	Thermo Fisher Scientific	Cat#12634010
B27 supplement	Thermo Fisher Scientific	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
SB202190	Sigma-Aldrich	Cat#S7067
A83-01	TOCRIS	Cat#2939
Primocin	Invivogen	Cat#ant-pm-1
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
Lysotracker Deep Red	Invitrogen	Cat#L12492
KaryoMAX™ Colcemid™ Solution in PBS	GIBCO	Cat#15212012
EMbed812	Electron Microscopy Science	Cat#EMS14120
Glutaraldehyde	Sigma-Aldrich	Cat#G5882
4% Paraformaldehyde	Biosesang	Cat#PC2031-050-00
Antifade mounting medium	VECTASHIELD	Cat#H-1000-10
Rapiclear®	SUNJin Lab	Cat#RC152001
FSC22 Frozen section	Leica	Cat#3801480
Triton X-100	Sigma-Aldrich	Cat#T9284-100ML
Normal donkey serum	Jackson immuno	Cat#NC9624464
Sucrose	Sigma-Aldrich	Cat#S0389-500G
Bovine Serum Albumin solution	Sigma-Aldrich	Cat#AB412-100ML
TrypLE Select	GIBCO	Cat#12563-029
TRIzol	Thermo Fisher Scientific	Cat#15596026
Critical Commercial Assays
C-chip Neubauer improved	iNCYTO	Cat#DHC-01
SuperScript IV	Thermo Fisher Scientific	Cat#18091050
Power SYBR Green PCR Master Mix	Thermo Fisher Scientific	Cat#4367659
RNeasy Plus Mini Kit	QIAGEN	Cat#74134
QIAamp Viral RNA Mini Kit	QIAGEN	Cat#52906
QIAquick PCR Purification Kit	QIAGEN	Cat#28106
pGEN-T Easy Vector Systems	Promega	Cat#A1360
RiboMAX Large Scale RNA Production Systems with T7	Promega	Cat#P1300
NucleoSpin RNA, Mini kit for RNA purification	MACHEREY-NAGEL	Cat#740955.50
Chromium Single cell 3′ GEM, Library & Gel Bead kit v3	10X Genomics	Cat#PN-1000075
Truseq Stranded Total RNA Gold kit	Illumina	Cat#20020599
CellTiter-Glo 3D Cell Viability Assay	Promega	Cat#G9681
LDH-Glo Cytotoxicity Assay	Promega	Cat#J2380
Deposited Data
h3AC and h3BC bulk RNA sequencing data	This paper	EGA: EGAS00001004508
Vero cell bulk RNA sequencing	This paper	GEO: GSE159316
h3AC single cell RNA sequencing data	This paper	EGA: EGAS00001004508
h3AC and h3BC transmission electron microscopy images	This paper	EMPIAR-10533
Supplemental information of this study	This paper	https://doi.org/10.17632/hzbrzdkcfr.1
Experimental Models: Cell Lines
Monkey: Vero cell (female)	Kim et al., 2020b	RRID:CVCL_0059
Human: 293T-HA-Rspo1-Fc cell	Trevigen	Cat#3710-000-01
Oligonucleotides
See Table S7. List of quantitative PCR primers		N/A
Software and Algorithms
FACSDiva software version(ver. 6.1.3)	BD Biosciences	N/A
FlowJo software	Tree Star, Inc	N/A
R (ver. 3.6.0)	Comprehensive R Archive Network	https://cran.r-project.org
Python (ver. 2.7.16)	Python Software Foundation	https://www.python.org/
Cell Ranger (ver. 3.1.0)	10X Genomics	Ver. 3.1.0; RRID:SCR_017344
Subset-bam	10X Genomics	https://github.com/10XGenomics/subset-bam
Seurat (v3)	Stuart et al., 2019	https://satijalab.org/seurat; RRID:SCR_016341
SC3	Kiselev et al., 2019	https://github.com/hemberg-lab/SC3; RRID:SCR_015953
Enhanced Volcano	Blighe et al., 2018	https://github.com/kevinblighe/EnhancedVolcano
ComplexHeatmap	Gu et al., 2016	https://github.com/jokergoo/ComplexHeatmap
Samtools (ver. 1.9)	Kiselev et al., 2019; Li et al., 2009	http://www.htslib.org; RRID:SCR_002105
Varscan2 (ver. 2.4.2)	Koboldt et al., 2012	http://dkoboldt.github.io/varscan/; RRID:SCR_006849
Strelka2 (ver. 2.9.2)	Saunders et al., 2012	https://sites.google.com/site/strelkasomaticvariantcaller/home; RRID:SCR_005109
Integrated Genomics Viewer	Robinson et al., 2011	http://software.broadinstitute.org/software/igv/
STAR (ver. 2.6.1)	Dobin et al., 2013	https://github.com/alexdobin/STAR; RRID:SCR_015899
RSEM (ver. 1.3.1)	Li and Dewey, 2011	https://github.com/deweylab/RSEM; RRID:SCR_013027
DESeq2	Love et al., 2014	http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html; RRID:SCR_015687
Enrichr	Kuleshov et al., 2016	https://maayanlab.cloud/Enrichr/
ZEN	ZEISS	Ver. 2.3
Tecnai Microscope control software	FEI	Ver. 4.17 SP1
SoftMax Pro software	Molecular Devices	N/A
Cytovision	Leica	Ver 7.4
Other
Nunc Lab-Tek II Chamber Slide System	Thermo Fisher Scientific	Cat#154534
SPL Collagen Type I Coated Ware	SPL	Cat#30208
Monkey reference genome, ChlSab1.1	Ensembl release 100	ftp://ftp.ensembl.org/pub/release-100/fasta/chlorocebus_sabaeus/dna/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa.gz
SARS-CoV-2 reference sequence, NC_045512.2	NCBI Reference Sequence	https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta
Human reference genome, GRCh38.p13	Ensembl release 100	ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
SARS-CoV-2 uninfected and infected human lung bulk RNA sequencing data	Blanco-Melo et al., 2020	GEO: GSE147507
SARS-CoV-2 uninfected and infected 2D cell line bulk RNA sequencing data	Emanuel et al., 2020a	GEO: GSE148729