REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
Wild-type SARS-CoV-2 isolate	Jonas Klingström	N/A
501Y.V2 isolate	Alex Sigal	Cele et al.34
Biological samples
Plasma from NHPs	This study	N/A
Chemicals, peptides, and recombinant proteins
Recombinant SARS-CoV-2 WT Spike	This study	N/A
Recombinant SARS-CoV-2 501Y.V2 RBD	This study	N/A
Polyethylenimine	Sigma-Aldrich	Cat# 764604
Matrix-M	Novavax AB	N/A
Lipofectamine 3000	Invitrogen	Cat# L3000075
Bright-Glo Luciferase Assay System	Promega	Cat# E2620
TRIzol Reagent	Thermo Fisher Scientific	Cat# 15596026
GlycoBlue Coprecipitant	Thermo Fisher Scientific	Cat# AM9515
SuperScript III One-Step RT-PCR System with Platinum Taq DNA Polymerase	Thermo Fisher Scientific	Cat# 12574018
mMESSAGE mMACHINE T7 Transcription Kit	Thermo Fisher Scientific	Cat# AM1344
GIBCO FreeStyle MAX Reagent	Thermo Fisher Scientific	Cat# 16447100
Gibson Assembly Mastermix	New England Biolabs	Cat# E2611S
Deposited data
SARS-CoV-2 lineage metadata	GISAID	https://www.gisaid.org
Experimental models: cell lines
Human: GIBCO FreeStyle 293-F cells	Thermo Fisher Scientific	Cat# R79009
Human: HEK293T-ACE2	Hanke et al.35	N/A
Human: Calu-3	Jonas Klingström	N/A
African Green Monkey: Vero E6 cell	ATCC	Cat# CRL-1586; RRID: CVCL_0574
Experimental models: organisms/strains
NHP: Macaca mulatta	N/A	N/A
Mouse: K18-hACE2	Jackson Laboratory, McCray et al.24	Cat# 034860; RRID: MSR_JAX:034860
Oligonucleotides
gBlocks Gene Fragments	Integrated DNA Technologies	N/A
Recombinant DNA
SARS-CoV-2 Spike ectodomain plasmid (expression)	Hsieh et al.36	Addgene: 154754; RRID: Addgene_154754
SARS-CoV-2 B.1.351/501Y.V2 RBD plasmid	This study	N/A
SARS-CoV-2 WT Spike plasmid	James Voss	Rogers et al.37
SARS-CoV-2 B.1.1.7 Spike plasmid	David Nemazee	Addgene: 170451; RRID: Addgene_170451
SARS-CoV-2 B.1.351 Spike plasmid	Penny Moore	Wibmer et al.38
SARS-CoV-2 P.1 Spike plasmid	David Nemazee	Addgene: 170450; RRID: Addgene_170450
SARS-CoV-2 B.1.617.2 Spike plasmid	G2P-UK National Virology consortium	Spencer et al.39
SARS-CoV-1 Spike plasmid	James Voss	Rogers et al.37
Lentiviral backbone: pCMV delta R8.2	Bob Weinberg	Addgene: 8455; RRID: Addgene_8455
Luciferase transfer plasmid	James Voss	Rogers et al.37
Software and algorithms
GraphPad Prism v9.0.0	GraphPad Software Inc.	https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798
Julia v1.6	The Julia Programming Language	https://julialang.org/
Non-linear Multinomial Regression for VOC frequency estimation	This study	https://github.com/MurrellGroup/VOCfreq; https://doi.org/10.5281/zenodo.5562800
Other
HiLoad® 16/600 Superdex® 200 pg	Cytivia	Cat# 28-9893-35
His-Pur Ni-NTA resin	Thermo Fisher Scientific	Cat# 88222