REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-ACE2 antibody	R&D systems	Cat#AF933; RRID:AB_355722
Rabbit anti-SARS-CoV-2 S	Thermofisher	Cat#PA1-41165; RRID:AB_1087210
Mouse anti-SARS-CoV-2 S1	R&D systems	Cat#MAB105403
Mouse anti HIV-1 p55/p24	NIBSC	Cat#ARP313
Rabbit anti-GAPDH	Proteintech	Cat#10494-1-AP; RRID:AB_2263076
Anti-rabbit HRP conjugate	Cell Signaling	Cat#7074; RRID:AB_2099233
Anti-mouse HRP conjugate	Cell Signaling	Cat#7076; RRID:AB_330924
Goat anti-Rabbit IgG Alexa Fluor 647	Thermofisher	Cat#A21244; RRID:AB_2535812
Bacterial and virus strains
XL1-blue cells	Agilent	Cat#200249
Biological samples
Airway organoids	Joo-Hyeon Lee	N/A
Human Sera	Collier et al. (2021a)	N/A
Chemicals, peptides, and recombinant proteins
E64D	Tocris	Cat#4545
Camostat	Sigma-Aldrich	Cat#SML0057
Fugene HD Transfection Reagent	Promega	Cat#E2311
Fugene 6 Transfection Reagent	Promega	Cat#E2691
Critical commercial assays
Bright-Glo	Promega	Cat#E2650
QuikChange Lightning	Agilent	Cat#210518
QuantiTect SYBR Green PCR Kit	Qiagen	Cat#204143
Experimental models: Cell lines
HEK293T	ATCC	Cat#CRL-3216
HEK293T-TMPRSS2	Leo James	N/A
HEK293T-ACE2ΔTMPRSS2	Leo James	N/A
HEK293T-GFP11	Leo James	N/A
Vero-GFP1-10	Leo James	N/A
Vero-ACE2/TMPRSS2	Emma Thomson	N/A
Calu3	Paul Lehner	N/A
A549-ACE2/TMPRSS2	Massimo Palmarini	N/A
NCI-H1299	Simon Cook	N/A
HeLa-ACE2	James Voss	N/A
Oligonucleotides
SARS-CoV-2_Delta_G156E_Fwd: AG CTGGATGGAAAGCGAGGTGTACAG CAGCGCCAACAACTG	This paper	N/A
SARS-CoV-2_Delta_G156E_Rev: GC AGTTGTTGGCGCTGCTGTACACCT CGCTTTCCATCCAGCT	This paper	N/A
SARS-CoV-2_Delta_D142G_Fwd: G CAACGACCCCTTCCTGGGCGTCTA CTACCACAAGAAC	This paper	N/A
SARS-CoV-2_Delta_D142G_Rev: GT TCTTGTGGTAGTAGACGCCCAGGA AGGGGTCGTTGC	This paper	N/A
SARS-CoV-2_Delta_157F158R_Fwd: GCTGGATGGAAAGCGGGTTCCGGG TGTACAGCAGCGCC	This paper	N/A
SARS-CoV-2_Delta_157F158R_Rev: G GCGCTGCTGTACACCCGGAACCCGC TTTCCATCCAGC	This paper	N/A
Recombinant DNA
Plasmid: p8.91	Kemp et al. (2021)	N/A
Plasmid: pCSFLW	Kemp et al. (2021)	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 WT	Meng et al. (2021); Mlcochova et al. (2021)	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 ΔH69V70	Meng et al. (2021)	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta	Mlcochova et al. (2021)	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Kappa	Mlcochova et al. (2021)	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.1	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.2	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta + KappaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Kappa + DeltaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 WT + DeltaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 WT + KappaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.1 + DeltaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.2 + DeltaNTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.1 + BA.2NTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 BA.2 + BA.1NTD	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta+681H/P	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta + KappaNTD+681H/P	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta D142G	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta G156E	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 Delta 157F158R	This paper	N/A
Plasmid: pcDNA-SARS-CoV-2-D614G-S-Δ19 KappaRBD	Ferreira et al. (2021)	N/A
Software and algorithms
GraphPad Prism	GraphPad Software	Version 9.4.0
FlowJo10	FlowJo	https://www.flowjo.com/solutions/flowjo/downloads
ImageJ	NIH	https://imagej.nih.gov/ij/
Other
RNA (MS2)	Roche	Cat#10165948001
HIV RT	Milipore	Cat#382129
HindIII	NEB	Cat#R0104S
NheI	NEB	Cat#R3131S
Bsu36I	NEB	Cat#0524S