REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SARS-CoV-2 spike antibody (biotin, CR3022)	Novus Biologicals	Cat#CR3022; RRID:AB_2848080
Goat anti-monkey IgG (H+L) secondary antibody, HRP (polyclonal)	Invitrogen	Cat#PA1-84631; RRID:AB_933605
B1-182	Vaccine Research Center, NIH (Wang et al., 2021a)	N/A
A19-46.1	Vaccine Research Center, NIH (Wang et al., 2021a)	N/A
A19-61.1	Vaccine Research Center, NIH (Wang et al., 2021a)	N/A
S309	(Pinto et al., 2020)	N/A
A23-97.1	Vaccine Research Center, NIH (Corbett et al., 2021a)	N/A
A23-80.1	Vaccine Research Center, NIH (Corbett et al., 2021a)	N/A
Goat anti-human IgD-FITC (polyclonal)	Southern Biotech	Cat#2030-02; RRID:AB_2795624
PerCP-Cy5.5 mouse anti-human IgM (clone G20-127)	BD Biosciences	Cat#561285; RRID:AB_10611998
DyLight 405 AffiniPure goat anti-human serum IgA, α chain specific (polyclonal)	Jackson ImmunoResearch	Cat#109-475-011; RRID:AB_2337789
Brilliant Violet 570 anti-human CD20 antibody (clone 2H7)	Biolegend	Cat#302332; RRID:AB_2563805
Brilliant Violet 650 anti-human CD27 antibody (clone O323)	Biolegend	Cat#302828; RRID:AB_2562096
Brilliant Violet 785 anti-human CD14 antibody (clone M5E2)	Biolegend	Cat#301840; RRID:AB_2563425
BUV496 mouse anti-human CD16 (clone 3G8)	BD Biosciences	Cat#612944; RRID:AB_2870224
BUV737 mouse anti-human CD4 (clone SK3)	BD Biosciences	Cat#612748; RRID:AB_2870079
CD19-APC (clone J3-119)	Beckman Coulter	Cat#IM2470U
Alexa Fluor 700 mouse anti-human IgG (clone G18-145)	BD Biosciences	Cat#561296; RRID:AB_10612406
APC-Cy7 mouse anti-human CD3 (clone SP34-2)	BD Biosciences	Cat#557757; RRID:AB_396863
Anti-human CD38 PE (clone OKT10)	Caprico Biotechnologies	Cat#100826
PE-Cy5 mouse anti-human CD21 (clone B-ly4)	BD Biosciences	Cat#551064; RRID:AB_394028
Mouse anti-human CD185 (CXCR5) monoclonal antibody, PE-Cyanine7, eBioscience (clone MU5UBEE)	ThermoFisher Scientific	Cat#25-9185-42; RRID:AB_2573540
Mouse anti-human CD4 monoclonal antibody, PE-Cyanine5.5 (clone S3.5)	ThermoFisher Scientific	Cat#MHCD0418; RRID:AB_10376013
Brilliant Violet 570 anti-human CD8a antibody (clone RPA-T8)	Biolegend	Cat#301038; RRID:AB_2563213
PE-Cy5 mouse anti-human CD45RA (clone 5H9)	BD Biosciences	Cat#552888; RRID:AB_394517
Brilliant Violet 650 anti-human CD197 (CCR7) antibody (clone G043H7)	Biolegend	Cat#353234; RRID:AB_2563867
Mouse anti-human CD185 (CXCR5) monoclonal antibody, PE, eBioscience (clone MU5UBEE)	ThermoFisher Scientific	Cat#12-9185-42; RRID:AB_11219877
BV711 mouse anti-human CD183 (clone 1C6/CXCR3)	BD Biosciences	Cat#563156; RRID:AB_2738034
BUV737 mouse anti-human CD279 (PD-1) (clone EH12.1)	BD Biosciences	Cat#565299; RRID:AB_2739167
PE/Cyanine7 anti-human/mouse/rat CD278 (ICOS) antibody (clone C398.4A)	Biolegend	Cat#313520; RRID:AB_10643411
Mouse anti-human CD69-ECD, RUO (clone TP1.55.3)	Beckman Coulter	Cat#6607110; RRID:AB_1575978
Alexa Fluor 700 anti-human IFN-γ antibody (clone B27)	Biolegend	Cat#506516; RRID:AB_961351
BV750 rat anti-human IL-2 (clone MQ1-17H12)	BD Biosciences	Cat#566361; RRID:AB_2739710
High parameter custom BB700 conjugate (rat anti-human IL-4) (clone MP4-25D2)	BD Biosciences	Cat#624381
FITC mouse anti-human TNF (clone MAb11)	BD Biosciences	Cat#554512; RRID:AB_395443
BV421 rat anti-human IL-13 (clone JES10-5A2)	BD Biosciences	Cat#563580; RRID:AB_2738290
Brilliant Violet 605 anti-human IL-17A antibody (clone BL168)	Biolegend	Cat#512326; RRID:AB_2563887
Alexa Fluor 647 mouse anti-human IL-21 (clone 3A3-N2.1)	BD Biosciences	Cat#560493; RRID:AB_1645421
Brilliant Violet 785 anti-human CD154 antibody (clone 24-31)	Biolegend	Cat#310842; RRID:AB_2572187
SARS-CoV-2 (COVID-19) nucleocapsid antibody (polyclonal)	GeneTex	Cat#GTX135357; RRID:AB_2868464
Bacterial and virus strains
SARS-CoV-2 B.1.1.529 (challenge stock)	This paper	N/A
SARS-CoV-2 D614G (EHC-083E)	Mehul Suthar, Emory (Edara et al., 2021a)	N/A
SARS-CoV-2 B.1.351	Mehul Suthar, Emory (Vanderheiden et al., 2021)	N/A
SARS-CoV-2 B.1.617.2	Mehul Suthar, Emory (Edara et al., 2021b)	N/A
SARS-CoV-2 B.1.1.529 (neutralization assay)	Mehul Suthar, Emory (Edara et al., 2022)	N/A
Chemicals, peptides, and recombinant proteins
SARS-CoV2-WT-S2P-AVI-bio	Vaccine Research Center, NIH (Zhou et al., 2020)	N/A
SARS-CoV2-D614G-S2P-AVI-bio	Vaccine Research Center, NIH (Teng et al., 2021)	N/A
SARS-CoV2-B.1.351-S2P-AVI-bio	Vaccine Research Center, NIH (Teng et al., 2021)	N/A
SARS-CoV2-B.1.617.2-S2P-AVI-bio	Vaccine Research Center, NIH (Teng et al., 2021)	N/A
SARS-CoV2-B.1.1.529-S2P-AVI-bio	Vaccine Research Center, NIH (Teng et al., 2021)	N/A
MSD blocker A kit	Meso Scale Diagnostics	Cat#R93AA
MSD SULFO-TAG human ACE2 protein (included in kit)	Meso Scale Diagnostics	Cat#K15586U
MSD GOLD read buffer B	Meso Scale Diagnostics	Cat#R60AM
MSD diluent 100	Meso Scale Diagnostics	Cat#R50AA
Lipofectamine 3000 transfection reagent	ThermoFisher Scientific	Cat#L3000075
FuGENE 6 transfection reagent	Promega	Cat#E2691
Luciferase assay system	Promega	Cat#E1500
SARS-CoV-2 S-2P (Avidity and Epitope Mapping)	Vaccine Research Center, NIH (Corbett et al., 2021b; Francica et al., 2021)	N/A
SARS-CoV-2 B.1.1.529 S-2P (Avidity and Epitope Mapping)	Vaccine Research Center, NIH	N/A
Sodium thiocyanate solution	Millipore-Sigma	Cat#80518-500ML-F
BV605 Streptavidin	BD Biosciences	Cat#563260
BUV661 Streptavidin	BD Biosciences	Cat#612979
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit	ThermoFisher Scientific	Cat#L34966
PepMix SARS-CoV-2 (S1+S2) (custom p.K986P and p.V987P)	JPT Peptide Techologies	N/A
PepMix SARS-CoV-2 (Spike B.1.1.529 / Omicron)	JPT Peptide Techologies	Cat#PM-SARS2-SMUT08-1
Critical commercial assays
NEBNext ultra II RNA library prep kit for Illumina	New England Biolabs	Cat#E7770
NEBNext multiplex oligos	New England Biolabs	Cat#E6440
V-PLEX SARS-CoV-2 panel 22 (IgG) kit	Meso Scale Diagnostics	Cat#K15559U
V-PLEX SARS-CoV-2 panel 23 (IgG) kit	Meso Scale Diagnostics	Cat#K15567U
Britelite plus reporter gene assay system	PerkinElmer	Cat#6066769
His capture kit type 2	Cytiva	Cat#29234602
Amine coupling kit	Cytiva	Cat#BR100633
Series S sensor chip CM5	Cytiva	Cat#29149603
RNAzol BD Column Kit	Molecular Research Center	Cat#RC 292
TaqMan Fast Virus 1-Step Master Mix	ThermoFisher Scientific	Cat#4444436
Experimental models: Cell lines
Vero (clone E6)	ATCC	Cat#CRL-1586; RRID:CVCL_0574
VeroE6-TMPRSS2	Vaccine Research Center, NIH (Corbett et al., 2021c)	N/A
HEK-293T/17	ATCC	Cat#CRL-11268; RRID:CVCL_1926
HEK-293T-ACE2	Michael Farzan and Huihui Mu, Scripps Research	N/A
Experimental models: Organisms/strains
Indian-origin rhesus macaques	Vaccine Research Center, NIH	N/A
Oligonucleotides
Primer: sgLeadSARSCoV2_F: 5’-CGATCTCT TGTAGATCTGTTCTC-3’	Integrated DNA Technologies (Francica et al., 2021; Wolfel et al., 2020)	N/A
Probe: N2_P: 5’-FAM- CGATCAAAACAA CGTCGGCCCC-BHQ1 -3’	This paper	N/A
Primer: wtN_R: 5’-GGTGAACCAAGACGCA GTAT-3’	Integrated DNA Technologies (Corbett et al., 2021c; Saunders et al., 2021)	N/A
Recombinant DNA
VRC5601: pHR’CMV Luc	(Naldini et al., 1996)	N/A
VRC5602: pCMV ΔR8.2	(Naldini et al., 1996)	N/A
VRC9260: TMPRSS2	Vaccine Research Center, NIH (DiPiazza et al., 2021)	N/A
Spike_SARS-CoV-2 D614G	Vaccine Research Center, NIH (Corbett et al., 2021a)	N/A
Spike_SARS-CoV-2 B.1.351	Vaccine Research Center, NIH (Corbett et al., 2021a)	N/A
Spike_SARS-CoV-2 B.1.617.2	Vaccine Research Center, NIH (Corbett et al., 2021a)	N/A
Spike_SARS-CoV-2 B.1.1.529	Vaccine Research Center, NIH	N/A
Software and algorithms
CLC Genomics Workbench v.21.0.3	Qiagen	https://digitalinsights.qiagen.com/downloads/product-downloads/
Viridot program	(Katzelnick et al., 2018)	https://github.com/leahkatzelnick/Viridot
GraphPad Prism v8.2.0, v9.0.2, v9.2.0	GraphPad	https://www.graphpad.com/scientific-software/prism/
Biacore Insight Evaluation Software	Cytiva	Cat#29310602
FlowJo v10.7.2, v10.8.0	Becton Dickinson	https://www.flowjo.com
R v4.1.0	The R Foundation	https://www.r-project.org
Other
Amicon Ultra-15 centrifugal filter unit (50,000 MWCO)	Millipore Sigma	Cat#UFC905096
Streptavidin multi array 384 well plate	Meso Scale Diagnostics	Cat#L21SA-1