REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SARS-CoV-2 Spike	GeneTex	Cat# 632604; RRID: AB_2864418
SARS-CoV-2 Nucleoprotein	Sino Biological	Cat# 40143-R019; RRID: AB_2827973
DHODH	Santa Cruz	Cat# sc-166348; RRID: AB_2091729
HSC70	Santa Cruz	Cat# sc7298; RRID: AB_627761
J2/dsRNA:	Millipore	Cat# MABE1134; RRID: AB_2819101
Alexa Fluor 488 donkey anti-mouse	Thermo Fisher Scientific	Cat# A21202; RRID: AB_141607
Alexa Fluor 488 goat anti-mouse	Thermo Fisher Scientific	Cat# A11001; RRID: AB_2534069
Alexa Flour 546 donkey anti-rabbit	Thermo Fisher Scientific	Cat# A10040; RRID: AB_2534016
Donkey anti-mouse IgG, HRP conj.	Jackson ImmunoResearch	Cat# 715036,150; RRID: AB_2340773
Donkey anti-rabbit IgG, HRP conj.	Jackson ImmunoResearch	Cat# 711036152; RRID: AB_2340590
Bacterial and virus strains
SARS-CoV-2 ‘wildtype’, Göttingen/Germany	Isolated from patient (Stegmann et al., 2021a)	N/A
hCoV-19/Germany/BY-Bochum-1/2020	Isolated from patient (Meister et al., 2021)	GISAID: EPI_ISL_1118929
SARS-CoV-2 Germany/BavPat1/2020 (BavPat1)	Friedrich Loeffler Institute (Germany)	GISAID: EPI_ISL_406862
SARS-CoV-2 Alpha (B.1.1.7)	Robert Koch Institute (Berlin, Germany)	GISAID: EPI_ISL_751799
SARS-CoV-2 Beta (B.1.351)	Robert Koch Institute (Berlin, Germany)	GISAID: EPI_ISL_803957
SARS-CoV-2 Delta (B.1.617.2)	Robert Koch Institute (Berlin, Germany)	GISAID: EPI_ISL_2378732
Chemicals, peptides, and recombinant proteins
β-D-N4-Hydroxycytidine (NHC/EIDD-1931)	Cayman Chemical	Cat# 9002958
IMU-838	Immunic Therapeutics	N/A
BAY2402234	Selleckchem	Cat# S8847
Teriflunomide	Selleckchem	Cat# S4169
Teriflunomide	Biozol	Cat# CBS-FT16895
ASLAN003	Selleckchem	Cat# S9721
Brequinar	Selleckchem	Cat# S6626
Uridine	Selleckchem	Cat# S2029
Cytidine	Selleckchem	Cat# S2053
Molnupiravir	MedChemExpress LLC	Cat# HY-135853
DMSO	Applichem	Cat# A3672.0100
Crystal violet	Roth	Cat# T123.1
Methanol	Roth	Cat# 8388.3
Lysis Binding buffer (from MagNA Pure LC Total Nucleic Acid Isolation Kit)	Roche	Cat# 03038505001
Trizol LS	Life Technologies	Cat# 10296028
Trichlormethan/Chloroform	Applichem	Cat# 3313.1
Isopropanol	Applichem	Cat# 6752.2
Ethanol	ChemSolute/Th.Geyer	Cat# 11647081/2246
Triton X-100	Applichem	Cat# A1388
Nuclease free water	Ambion	Cat# AM9939
PEG400	Roth	Cat# 0144.1
Tween-80	Sigma Aldrich	Cat# P4780
Peanut Oil	Braendle	Cat# 913 or EAN# 4,008,722,009,130
Strawberry Syrup	Yo	EAN# 9001400005009
4′,6-Diamidino-2- Phenylindole (DAPI)	Sigma	Cat# D9542-5MG
Fluorescence Mounting Medium (DAKO)	DakoCytomation	Cat# S302380-2
Shandon Immu-Mount	Thermo Fisher Scientific	Cat# 9990402
Hoechst33342	Thermo Fisher Scientific	Cat# H3570
Formalin	Roth	Cat# 7398.1
Paraffin	VWR	Cat# 1071642504
Hematoxylin	Roth	Cat# 3816.1
Eosin (HE)	Th. Geyer, RV	Cat# E6003-25G
Critical commercial assays
Pierce BCA Protein Assay Kit	Thermo Fisher Scientific	Cat# 23227
Immobilon Western Substrate	Millipore	Cat# WBKLS0500
Super Signal West Femto Maximum Sensitivity Substrate	Thermo Fisher Scientific	Cat# 34095
LDH-GloTM Cytotoxicity Assay kit	Promega	Cat# J2380
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	Cat# G7570
StemDiff™ Branching Lung Organoid Kit	Stemcell	Cat# 100-0195
NucleoMag®VET kit	Machery & Nagel GmbH	Cat# 744200.4
QIAamp Viral RNA Mini Kit	Qiagen	Cat# 52904
TaqMan® Fast Virus 1-Step Master Mix	Thermo Fisher Scientific	Cat# 4444432
AgPath-ID One-Step RT-PCR Kit	Applied Biosystems	Cat# AM1005
Experimental models: Cell lines
Monkey: Vero E6 (Vero C1008)	ATCC	Cat# CRL-1586
Human: Calu-3	ATCC	Cat# HTB55
CD34-positive human induced pluripotent stem cells (hiPSCs)	Dorn et al. (2015)	N/A
Experimental models: Organisms/strains
Syrian Gold hamsters	Janvier Labs, Saint Berthevin, France	N/A
C57BL/6 mice	Janvier Labs, Saint Berthevin, France	N/A
K18-hACE-2 mice	Charles River Laboratories	704K18-HACE2
Oligonucleotides
Primer (probe), with 5′FAM, 3′BBQ ACA CTA GCC ATC CTT ACT GCG CTT CG	Eurofins Genomics	N/A
Primer (forward) ACA GGT ACG TTA ATA GTT AAT AGC GT	Eurofins Genomics	N/A
Primer (reverse) ATA TTG CAG CAG TAC GCA CAC A	Eurofins Genomics	N/A
Software and algorithms
Prism (version 9.0.0)	GraphPad	N/A
SynergyFinder	Zheng et al. (2022)	https://synergyfinder.org
AxioVision Zen 2 (2.0.0.0)	Zeiss	N/A
Image Lab™ (version 5.2.1)	Bio-Rad	N/A
BioRender	BioRender	https://biorender.com/
SPSS (version 20.0)	SPSS Inc.	N/A
NDPview.2 plus (version 2.8.24)	Hamamatsu Photonics, K.K. Japan	N/A