REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Casirivimab	Regeneron Pharmaceuticals	N/A
Imdevimab	Regeneron Pharmaceuticals	N/A
Casirivimab + Imdevimab cocktail	Regeneron Pharmaceuticals	N/A
Bamlanivimab	Discarded vials, NYU Langone Health	N/A
Etesevimab	Discarded vials, NYU Langone Health	N/A
Bamlanivimab + Etesevimab cocktail	Discarded vials, NYU Langone Health	N/A
Bebtelovimab	Discarded vials, NYU Langone Health	N/A
Tixagevimab	Discarded vials, NYU Langone Health	N/A
Cilgavimab	Discarded vials, NYU Langone Health	N/A
Tixagevimab + Cilgavimab cocktail	Discarded vials, NYU Langone Health	N/A
Sotrovimab	Discarded vials, NYU Langone Health	N/A
Bacterial and virus strains
Infectious SARS-CoV-2 Delta-Omicron	This study	N/A
Infectious SARS-CoV-2 Delta	This study	N/A
Infectious SARS-CoV-2 BA.1	This study	N/A
SARS-CoV-2 Δ19 SD614G pseudotyped reporter virus	Tada et al.32	N/A
SARS-CoV-2 Δ19 S Delta pseudotyped reporter virus	Tada et al.33	N/A
SARS-CoV-2 Δ19 S BA.1 pseudotyped reporter virus	Tada et al.34	N/A
SARS-CoV-2 Δ19 S BA.2 pseudotyped reporter virus	Zhou et al.35	N/A
SARS-CoV-2 Δ19 S Delta-Omicron pseudotyped reporter virus	This paper	N/A
Biological samples
Sera from individuals vaccinated with BNT162b2. See Table S4	NYU Vaccine Center with written consent under Institutional Review Board approval	Deidentified, IRB 20-00595 and IRB 18-02037
Chemicals, peptides, and recombinant proteins
Polyethyleneimine	Polysciences	Cat# 23966-1
Luciferase substrate	NanoLight Technology	Cat# 325-50
Critical commercial assays
GIBCO ExpiFectamine Transfection Kits	Thermo Fisher Scientific	Cat# A29130
Nano-Glo® Luciferase Assay System	Promega	Cat# N1120
Deposited data
Full genome sequence of SARS-CoV-2 Delta-Omicron recombinant virus	GISAID	EPI_ISL_10792641
xGen and shotgun deep sequencing data (raw fastq files; NYU). See Table S1	NCBI SRA	PRJNA915368
AmpliSeq, harvest and 24h–96h in vitro culture deep sequencing data (raw fastq files; NY State DOH). See Table S1	NCBI SRA	PRJNA915368
Experimental models: Cell lines
VeroE6/TMPRSS2 cells	JCRB Cell Bank	JCRB1819
293T cells	ATTC	CRL-3216™
ACE2.293T cells	Tada et al.32	N/A
Oligonucleotides
Primers. See Table S3	This study	IDT
Recombinant DNA
HIV-1 Gag/Pol expression vector pMDL	Tada et al.32	N/A
HIV-1 Rev expression vector pRSV.Rev	Tada et al.32	N/A
Lentiviral reporter vector pLenti.GFP-NLuc	Tada et al.32	N/A
Synthesized cDNA fragment, SARS-CoV-2 Delta-Omicron recombinant spike. See Table S3	This study	GenScript
SARS-CoV-2 Δ19 S D614G spike plasmid	Tada et al.32	N/A
SARS-CoV-2 Δ19 S D614G spike P337L plasmid	This study	N/A
SARS-CoV-2 Δ19 S D614G spike E340A plasmid	This study	N/A
SARS-CoV-2 Δ19 S D614G spike E340D plasmid	This study	N/A
SARS-CoV-2 Δ19 S D614G spike E340K plasmid	This study	N/A
SARS-CoV-2 Δ19 S D614G spike E340V plasmid	This study	N/A
SARS-CoV-2 Δ19 S Delta spike plasmid	Tada et al.33	N/A
SARS-CoV-2 Δ19 S BA.1 spike plasmid	Tada et al.34	N/A
SARS-CoV-2 Δ19 S BA.2 spike plasmid	Zhou et al.35	N/A
SARS-CoV-2 Δ19 S Delta-Omicron spike plasmid	This study	N/A
SARS-CoV-2 Δ19 S BA.1 spike E340D plasmid	This study	N/A
SARS-CoV-2 Δ19 S Delta-Omicron spike D340E plasmid	This study	N/A
Software and algorithms
GraphPad Prism 8.0e	GraphPad Prism Software, Inc.	N/A
IQ-TREE v2.2.0	IQ-TREE	N/A
BEAST v1.10.5	BEAST	N/A
Nextstrain CLI v6.0.0	Nextstrain	N/A
Nextclade v1.14	Nextclade	N/A
Swiss-Model	Swiss-Model	N/A
UCSF ChimeraX 1.3	UCSF Chimera	N/A
BioRender	BioRender	N/A