REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
purified NA/LE mouse anti-human CD28 (clone 28.2)	BD PharMingen	Cat# 555725; RRID: AB_2130052
purified NA/LE mouse anti-human CD49d (clone L25)	BD PharMingen	Cat# 555501; RRID: AB_396068
LIVE/DEAD™ Fixable VIVID Stain	Invitrogen	Cat# L34955
CD14 Pac Blue (clone TuK4)	Invitrogen Thermofisher Scientific	Cat# MHCD1428; RRID: AB_10373537
CD19 Pac Blue (clone SJ25-C1)	Invitrogen Thermofisher Scientific	Cat# MHCD1928; RRID: AB_10373689
CD4 PERCP-Cy5.5 (clone L200)	BD Biosciences	Cat# 552838; RRID: AB_394488
CD8 BV510 (clone RPA-8)	Biolegend	Cat# 301048; RRID: AB_2561942
PD-1 BV711 (clone EH12.2H7)	Biolegend	Cat# 329928; RRID: AB_11218612
CD27 PE-Cy5 (clone 1A4)	Beckman Coulter	Cat# 6607107; RRID: AB_10641617)
CD45RA BV570 (clone HI100)	Biolegend	Cat# 304132; RRID: AB_2563813
CD3 BV650 (clone OKT3)	Biolegend	Cat# 317324; RRID: AB_2563352
IFN-g Alexo 700 (clone B27)	BD Biosciences	Cat# 557995; RRID: AB_396977
TNF BV786 (clone Mab11)	Biolegend	Cat# 502948; RRID: AB_2565858
IL-2 APC (clone MQ1-17H12)	Biolegend	Cat# 500310; RRID: AB_315097
CR3022	Genscript (https://www.genscript.com)	N/A
BD23	Dr Nicole Doria-Rose, VRC, USA	N/A
P2B-2F6	Dr Nicole Doria-Rose, VRC, USA	N/A
anti-IgG APC (clone QA19A42)	Biolegend	Cat#366905 RRID: AB_2888847
Palivizumab	Medimmune	Synagis; RRID: AB_2459638
Bacterial and virus strains
SARS-CoV-2 pseudoviruses for ancestral, Beta and Delta	Wibmer et al., 2021; This paper	N/A
Biological samples
Convalescent health care worker blood samples	Groote Schuur Hospital	https://www.gsh.co.za
Chemicals, peptides, and recombinant proteins
PepTivator® SARS-CoV-2 Prot_S	Miltenyi Biotech	Cat #130-126-701
PepTivator® SARS-CoV-2 Prot_S1	Miltenyi Biotech	Cat# 130-127-048
SARS-CoV-2 Original Wuhan, Beta and Delta spike synthetic peptides	TC Peptide Lab	https://tcpeptidelab.com
SARS-CoV-2 original and Beta variant spike proteins	Original: Hsieh et al., 2020; Beta: Moyo-Gwete et al., 2021	N/A
Critical commercial assays
Superscript IV Reverse Transcriptase	Life Technologies, Carlsbad, CA	Cat # 18090200
Qubit dsDNA High Sensitivity assay	Life Technologies Carlsbad, CA	Cat # Q32854
AMPure XP magnetic beads	Beckman Coulter	Cat # A63881
Illumina® DNA Prep kit	Illumina, San Diego	Cat # 20018705
Nextera™ DNA CD Indexes (96 Indexes, 96 Samples)	Illumina, San Diego	Cat # 20018708
Elecsys anti-SARS-CoV-2 Spike immunoassay	Roche Diagnostics	CAT# 09 289 275 190
Elecys anti-SARS-CoV-2 electrochemiluminescent immunoassay	Roche Diagnostics	CAT# 09 203 095 190
PEI-MAX 40,000	Polysciences	Cat # 24765-1
LIVE/DEAD™ Fixable VIVID Stain	Invitrogen	Cat # L34955
Cytofix/Cyto perm buffer	BD Biosciences	Cat # 554722
CellFIX	BD Biosciences	Cat # 340181
QUANTI-Luc luciferase	Invivogen	Cat# rep-qlc2
Luciferase for neuts	Promega	Cat# PRE263B-C
Deposited data
PID1054 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621106
PID1127 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621118
PID1128 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GSAID Accession # EPI_ISL_2621122
PID1134 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_1534413
PID1169 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621117
PID1319 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621127
PID1337 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621124
PID1399 SARS-CoV-2 Viral sequence	GISAID EpiCoV database	GISAID Accession # EPI_ISL_2621110
Ancestral (Wuhan)	www.ncbi.nlm.nih.gov	NC_045512.2
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_660629
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736930
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736932
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736944
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736971
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736966
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_736973
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_825104
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_825120
B.1.351 (Beta)	www.GISAID.org	EPI_ISL_825131
B.1.617.2 (Delta)	www.GISAID.org	EPI_ISL_2020950
Experimental models: Cell lines
Human Embryonic Kidney (HEK) 293F	Dr Nicole Doria-Rose, VRC, USA	N/A
HEK293T-ACE2 cells	Dr Michael Farzan, Scripps, USA	N/A
Jurkat-Lucia™ NFAT-CD16 cells	Invivogen	Cat # jktl-nfat-cd16
Recombinant DNA
Spike Hexapro plasmid	Original: Hsieh et al., 2020Beta: Moyo-Gwete et al., 2021	N/A
SARS-CoV-2 ancestral variant spike (D614G) plasmid	Wibmer et al., 2021	N/A
Beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) plasmid	Wibmer et al., 2021	N/A
Delta spike (T19R, R158G L452R, T478K, D614G, P681R, D950N, 156-157 del) plasmid	This paper	N/A
Firefly luciferase encoding lentivirus backbone plasmid	Dr Michael Farzan, Scripps	N/A
Software and algorithms
Genome Detective 1.132	Genome Detective	https://www.genomedetective.com
Coronavirus Typing Tool	Cleemput et al., 2020	N/A
Geneious software	Biomatters Ltd	N/A
NextStrain	Hadfield et al., 2018	https://github.com/nextstrain/ncov
FACSDiva 9	BD Biosciences	https://www.bdbiosciences.com
FlowJo 10	FlowJo, LLC	https://www.flowjo.com
Graphpad Prism 9	Graphpad	https://graphpad.com
BioRender	BioRender	https://biorender.com