REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Oct-3/4	R and D Systems	Cat#AF1759; RRID:AB_354975
Anti-TEAD4	Abcam	Cat#ab58310; RRID:AB_945789
ENPEP	Abcam	Cat#ab155991; RRID:AB_2916048
Purified anti-human CD75 Antibody	BioLegend	Cat#326901; RRID:AB_2194435
Anti-KLF17 antibody	Sigma-Aldrich	Cat#HPA024629; RRID:AB_1668927
Recombinant Anti-active YAP1 antibody	Abcam	Cat#ab205270; RRID:AB_2813833
Anti-CDX2 antibody [EPR2764Y]	Abcam	Cat#ab76541; RRID:AB_1523334
GCM1 Antibody	Novus	Cat#NBP2-48520; RRID:AB_2916049
PE anti-human CD49e Antibody	BioLegend	Cat#328009; RRID:AB_893368
Purified anti-human/mouse CD49f Antibody	BioLegend	Cat#313602; RRID:AB_345296
FITC anti-human CD49a Antibody	BioLegend	Cat#328307; RRID:AB_1236430
Alexa Fluor® 488 anti-human HLA-A,B,C Antibody	BioLegend	Cat#311413; RRID:AB_493133
ENDOU Antibody	Novus biologicals	Cat#NBP2-55877; RRID:AB_2916050
Anti-E Cadherin [EP700Y]	Abcam	Cat#ab40772; RRID:AB_731493
Anti-Transcription factor AP-2-alpha [EPR2688(2)]	Abcam	Cat#ab108311; RRID:AB_10861200
Purified anti-human CD49e Antibody	BioLegend	Cat#328002; RRID:AB_8933
Anti-GATA-3	R and D Systems	Cat#MAB6330; RRID:AB_10640512
Anti-TRA-1-60	STEMCELL Technologies	Cat#60064; RRID:AB_2686905
Anti-ACE2	Thermo Fisher Scientific	Cat# MA5-32307; RRID:AB_2809589
ACE2 Rabbit mAb	ABclonal	Cat#A4612; RRID:AB_2863309
Anti-SSEA-4	STEMCELL Technologies	Cat#60062; RRID:AB_2721031
Anti-hCGB	Thermo Fisher Scientific	Cat#14-6508-82; RRID:AB_10853505
Anti-KRT7	Santa Cruz Biotechnology	Cat# sc-70936; RRID:AB_2234501
Anti-AP-2 gamma	R and D Systems	Cat#AF5059; RRID:AB_2255891
Anti-HLA-G	Abcam	Cat#ab7759; RRID:AB_306053
Anti-CD46	BioLegend	Cat#352403; RRID:AB_10897448
Anti-ZO-1	ABclonal	Cat#A0659; RRID:AB_2757321
Anti-KRT18	R and D Systems	Cat#MAB7619; RRID:AB_2893116
Alexa Fluor® 488 anti-human/mouse SSEA-3 Antibody	BioLegend	Cat#330305; RRID:AB_1279441
Alexa Fluor® 488 anti-human/mouse TRA-1-60 Antibody	BioLegend	Cat#330613; RRID:AB_2295395
Anti-p63/TP73L	R and D Systems	Cat#AF1916; RRID:AB_2207174
Donkey anti-Mouse 555	Thermo Fisher Scientific	Cat#A-31570; RRID:AB_2536180
Donkey anti-Mouse 488	Thermo Fisher Scientific	Cat#A-21202; RRID:AB_141607
Donkey anti-Goat 555	Thermo Fisher Scientific	Cat#A-21432; RRID:AB_2535853
Donkey anti-Goat 488	Thermo Fisher Scientific	Cat#A-11055; RRID:AB_2534102
Donkey anti-Rabbit 594	Thermo Fisher Scientific	Cat#A-21207; RRID:AB_141637
Donkey anti-Rabbit 488	Thermo Fisher Scientific	Cat#A-21206; RRID:AB_2535792
Goat anti-Guinea Pig 647	Thermo Fisher Scientific	Cat#A-21450; RRID:AB_141882
Bacterial and virus strains
SARS-CoV-2 (HKU-001a)	In house	GenBank: MT230904
SARS-CoV-2 Omicron	hCoV-19/Hong Kong/HKU-344/2021	GISAID: EPI_ISL_7357684
SARS-CoV-2 Delta	hCoV-19/Hong Kong/HKU-210804-001/2021	GISAID: EPI_ISL_3221329
MERS-CoV (EMC/2012)	Erasmus Medical Center, Netherlands	GenBank:JX869059.2
Top10 Competent Cell	TIANGEN	CB104-02
Chemicals, peptides, and recombinant proteins
GC376	MedChemExpress	HY-100721
CTS™ (Cell Therapy Systems) N-2 Supplement	Thermo Fisher Scientific	A1370701
B-27™ Supplement (50X), serum free	Thermo Fisher Scientific	17504044
XAV939	MedChemExpress	HY-15147
PD0325901	MedChemExpress	HY-10254
Gö 6983	MedChemExpress	HY-13689
Neurobasal Medium	Thermo Fisher Scientific	21103049
remdesivir	MedChemExpress	HY-104077
DMEM/F-12, no glutamine	Thermo Fisher Scientific	21331020
Y-27632 dihydrochloride	Tocris	1254/10
FBS	Thermo Fisher Scientific	10270
LIF Recombinant Human Protein	Thermo Fisher Scientific	PHC9484
DPBS, powder, no calcium, no magnesium	Thermo Fisher Scientific	21600010
FastQuant RT Super Mix	TIANGEN	KR108-01
PowerUp™ SYBR™ Green Master Mix	Thermo Fisher Scientific	A25776
SB-431542	Tocris	1614
A83-01	Tocris	2939
CHIR-99021	Tocris	4423
A 419259 trihydrochloride	MedChemExpress	HY-15764A
Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix	Thermo Fisher Scientific	A1413201
MicroAmp™ Fast Optical 96-Well Reaction Plate with Barcode, 0.1 mL	Thermo Fisher Scientific	4346906
MicroAmp™ Optical Adhesive Film	Thermo Fisher Scientific	4360954
Forskolin	Sigma-Aldrich	F3917
Matrigel Matrix. GFR	Corning	354230
EGF Recombinant Human Protein	Thermo Fisher Scientific	PHG0311
Prostaglandin E2	MedChemExpress	HY-101952
HGF Protein, Human, Recombinant	Sino biological	Cat: 10463-HNAS
RSPO1 Protein, Human, Recombinant	Sino biological	Cat: 11083-HNAS
DMSO, Anhydrous	Thermo Fisher Scientific	D12345
BSA solution	Sigma-Aldrich	A7979
Recombinant Human NRG1-beta 1/HRG1-beta 1 EGF Domain Protein	R and D Systems	396-HB-050
Normal Donkey Serum	Abcam	ab7475
Knockout serum replacement	Thermo Fisher Scientific	10828010
Valproic Acid (Sodium Salt)	Stem cell technology	72292
Cell Recovery Solution	Corning	354253
Recombinant Human FGF basic/FGF2/bFGF (146 aa) Protein	R and D Systems	233-FB-500/CF
μ-Slide 8 Well high Glass Bottom	ibidi	80807
b-Mercaptoethanol	Thermo Fisher Scientific	31350010
TryPLE-Express	Thermo Fisher Scientific	12605036
Trypsin/EDTA	Thermo Fisher Scientific	25200072
Penicillin-Streptomycin-Glutamine (100X)	Thermo Fisher Scientific	10378016
Minimum Essential Medium (MEM) Vitamin Solution	Thermo Fisher Scientific	11120052
Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (100X)	Thermo Fisher Scientific	51500056
Triton X-100	Sigma-Aldrich	T9284
4% Paraformaldehyde	Sigma-Aldrich	P6148
2-phospho-L-ascorbic-acid	Sigma-Aldrich	A8960-5G
Critical commercial assays
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	G7570
miRcute Plus miRNA cDNA First-Strand cDNA Kit	TIANGEN	KR211-01
miRcute Plus miRNA qPCR Kit (SYBR Green)	TIANGEN	FP411-01
QuantiNova Probe RT-PCR kit	QIAGEN	208354
Transwell invasion assay	Corning	354480
TUNEL cell apoptosis detection kit	Servicebio	G1501
Deposited data
RNA-seq data	(Okae et al., 2018)35	DDBJ: JGA00000000074
RNA-seq data	(Okae et al., 2018)35	DDBJ: JGA00000000117
RNA-seq data	(Okae et al., 2018)35	DDBJ: JGA00000000122
RNA-seq data	(Gao, ,2019)24	ARRAYEXPRESS: E-MTAB-7253
RNA-seq data	(Sheridan, 2021)	ARRAYEXPRESS: E-MTAB-10429
scRNA-seq data	(Zhou, et al., 2019)44	GEO: GSE109555
scRNA-seq data	(Liu, et al., 2018)45	GEO: GSE89497
RNA-seq data	This paper	GEO: GSE190432
scRNA analysis	This paper	https://github.com/leeyoyohku/EPSC_COVID
Experimental models: Cell lines
Monkey: Vero E6 cells	ATCC	CCL-81
Human embryonic stem cell (hESC) line: Man-1/M1	(Camarasa, 2010)	N/A
Caco-2 [Caco2]	ATCC	HTB-37
TSC-BST, Human Blastocyst derived hTSCs	(Okae et al., 2018)35	N/A
Oligonucleotides
Primers used, see Table S5	This paper	N/A
Software and algorithms
ImageJ Fiji (2.0.0)	NIH	https://imagej.net/Fiji
GraphPad Prism 8.0	GraphPad	https://www.graphpad.com/scientific- software/prism/
Microsoft	Microsoft	https://www.microsoft.com/de-at/microsoft- 365/excel
Synthego	N/A	https://ice.synthego.com/#/
BioRender	N/A	https://biorender.com/
Adobe Illustrator	Adobe	https://www.adobe.com/at/products/illustrator.html
FlowJo	BD Life Sciences	https://www.flowjo.com/
Zeiss Zen (Blue edition)	Zeiss	https://www.zeiss.com/microscopy/int/products/microscope-software/zen-lite.html
FeatureCounts v2.0.1	N/A	http://subread.sourceforge.net
SCANPY (v1.7.2, scRNA/integrative analysis)	N/A	https://scanpy-tutorials.readthedocs.io/en/latest/index.html