REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
N protein antibody	Abcam	cat# ab273434; RRID:AB_2893371
goat anti-mouse IgG H&L-Alexa fluor 488	Abcam	cat# ab150113; RRID:AB_2576208
mouse anti-Spike antibody	Abcam	cat# ab273433; RRID: AB 2891068)
Rabbit anti-mCherry antibody	Novus Biologicals	cat# nbp2-43720; RRID:AB_2893372
Goat anti-rabbit IgG (H+L) cross-adsorbed secondary antibody, Alexa fluor 405	Invitrogen	cat# a-31556, RRID:AB_221605
Bacterial and virus strains
SARS-CoV-2 isolate (USA-WA1/2020)	SARS-CoV-2 isolate (USA-WA1/2020) was deposited by the Centers for Disease Control and Prevention and obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate USA-WA1/2020.	NR-52281
SARS-CoV-2 variant 501Y.V2	SARS-CoV-2 variant 501Y.V2 was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/USA/MD-HP01542/2021 (Lineage B.1.351), in Homo sapiens Lung Adenocarcinoma (Calu-3) Cells, NR-55282, contributed by Andrew S. Pekosz.	NR- 54008
SARS-CoV-2 variant B1.1.7	SARS-CoV-2 variant B1.1.7 was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/England/204820464/2020, contributed by Bassam Hallis.	NR- 54000
SARS-CoV-2 variant 501YV2 HV Delta	SARS-CoV-2 variant 501YV2 HV Delta was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/USA/MD-HP01542/2021 (Lineage B.1.351), in Homo sapiens Lung Adenocarcinoma (Calu-3) Cells, NR-55282, contributed by Andrew S. Pekosz.	NR- 54009
Chemicals, peptides, and recombinant proteins
Advanced DMEM/F12	Invitrogen	12634010
HEPES	Invitrogen	15630-056
GlutaMAX	Invitrogen	35050061
Penicillin-Streptomycin	Invitrogen	15140-122
B27 supplement	Invitrogen	17504-044
N-acetylcysteine	Sigma	A9165
Nicotinamide	Sigma	N0636
Y-27632	Tocris	1254
A8301	Tocris	2939
FGF-7	Peprotech	100-19
FGF-10	Peprotech	100-26
Primocin	InvivoGen	ant-pm-1
Heregulin beta-1	Peprotech	100-03
SB202190	Sigma	S7067
Uranyl Formate	VWR International	16984-59-1
Hoechst stain	Thermofisher Scientific	H1399
Experimental models: Cell lines
Vero cells	ATCC	CRL-1586
Human small airway epithelial cells (HSAEpC)	PromoCell	C12642
Experimental models: Organisms/strains
Hamster / Golden Syrian Hamster / Male / 6-8 weeks old	Charles River	Strain Code 049
NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice/ female/ 7 weeks old	Jackson Laboratory	005557
Oligonucleotides
Gene block for TIP1	Integrated DNA Technology	N/A
Gene blocks for TIP2	Integrated DNA Technology	N/A
Primers: See Table S1	Integrated DNA Technology	N/A
Critical commercial assays
SE cell line 4D nucleofector kit	Lonza	V4XC-1012
Direct-zol RNA extraction kit	Zymo Research	R2070T
Illumina Stranded total RNA library prep kit	Illumina	20040525
HiScribe T7 high yield RNA synthesis kit	New England Biolabs	E2040S
Vaccinia Capping System	New England Biolabs	M2080S
E.coli Poly(A) polymerase	New England Biolabs Inc	M0276S
RNase free DNase-I	Thermofisher Scientific	EN0521
SuperScript II Reverse Transcriptase	Thermofisher Scientific	12574026
SYBR green PCR master mix	Thermofisher Scientific	4309155
TRIzol LS Reagent	Invitrogen	10296010
Lipofectamine 3000 transfection reagent	Thermofisher Scientific	L3000001
Recombinant DNA
pLVX-EF1alpha-SARS-CoV-2-N-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-nsp7-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-nsp8-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-nsp12-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-S-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-M-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pLVX-EF1alpha-SARS-CoV-2-E-2xStrep-IRES-Puro	(Gordon et al., 2020b)	N/A
pMAX GFP vector	Lonza	V4XC-1012
Software and algorithms
FlowJo	FlowJo	https://www.flowjo.com/
Prism	GraphPad	https://www.graphpad.com/
ImageJ	(Schneider et al., 2012)	https://imagej.nih.gov/ij/
MetaXpress	Molecular Devices	https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metaxpress
Integrated Genome Browser	Broad Institute	https://software.broadinstitute.org/software/igv/
Lago in-vivo Imaging System	Spectral Instruments Imaging	https://spectralinvivo.com/software/
Code and Raw Data	This paper	https://zenodo.org/record/5579847 Zenodo: 5579847
Deposited data
RNAseq Data	This paper	GEO: GSE184447https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184447