REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Ki-67-FITC human	BD Biosciences	BD Biosciences Cat# 556026; RRID:AB_396302, clone B56
CD4 Monoclonal Antibody (SK3 (SK-3)), PerCP-eFluor 710, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 46-0047-42; RRID:AB_1834401, clone SK3
Alexa Fluor 647 anti-human/mouse Granzyme B antibody	BioLegend	BioLegend Cat# 515406; RRID:AB_2566333, clone GB11
Alexa Fluor 700 anti-human IgM antibody	BioLegend	BioLegend Cat# 314538; RRID:AB_2566615, clone MHM-88
APC/Cyanine7 anti-human CD27 antibody	BioLegend	BioLegend Cat# 302816; RRID:AB_571977, clone O323
Mouse Anti-IgD Monoclonal Antibody, Phycoerythrin Conjugated, Clone IA6-2	BD Biosciences	BD Biosciences Cat# 555779; RRID:AB_396114, clone IA6-2
PE/Dazzle 594 anti-human CD56 (NCAM) antibody	BioLegend	BioLegend Cat# 318348; RRID:AB_2563564, clone HCD56
Mouse Anti-HLA-DR, DP, DQ Monoclonal Antibody, Unconjugated, Clone TU39	BD Biosciences	BD Biosciences Cat# 555557; RRID:AB_395939, clone TU39
PE/Cy5 anti-human CD19 antibody	BioLegend	BioLegend Cat# 302210; RRID:AB_314240, clone HIB19
CD38 Monoclonal Antibody (HIT2), PE-Cyanine7, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 25-0389-42; RRID:AB_1724057, clone HIT2
Brilliant Violet 421 anti-human CD185 (CXCR5) antibody	BioLegend	BioLegend Cat# 356920; RRID:AB_2562303, clone J252D4
Brilliant Violet 510 anti-human CD14 antibody	BioLegend	BioLegend Cat# 367123; RRID:AB_2716228, clone 63D3
Brilliant Violet 570 anti-human CD45RA antibody	BioLegend	BioLegend Cat# 304132; RRID:AB_2563813, clone HI100
Brilliant Violet 605 anti-human CD183 (CXCR3) antibody	BioLegend	BioLegend Cat# 353728; RRID:AB_2563157, clone G02H57
Brilliant Violet 650 anti-human CD20 antibody	BioLegend	BioLegend Cat# 302336; RRID:AB_2563806, clone 2H7
Brilliant Violet 711 anti-human CD197 (CCR7) antibody	BioLegend	BioLegend Cat# 353228; RRID:AB_2563865, clone G043H7
Brilliant Violet 785 anti-human CD279 (PD-1) antibody	BioLegend	BioLegend Cat# 329930; RRID:AB_2563443, clone EH12.2H7
BUV396 CD3 antibody human	BD Biosciences	BD Biosciences Cat# 563546; RRID:AB_2744387, clone UCHT1
BD Horizon BUV496 Mouse Anti-Human CD196 (CCR6) antibody	BD Biosciences	BD Biosciences Cat# 612948; RRID:AB_2833076, clone 11A9
BUV737 Mouse Anti-Human CD16 antibody	BD Biosciences	BD Biosciences Cat# 612786; RRID:AB_2833077, clone 3G8
BD Horizon BUV805 Mouse Anti-Human CD8 antibody	BD Biosciences	BD Biosciences Cat# 612889; RRID:AB_2833078, clone SK1
LIVE/DEAD Fixable Blue Dead Cell Stain Kit, for UV excitation	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# L34962
FITC anti-human CD69 antibody	BioLegend	BioLegend Cat# 310904; RRID:AB_314839, clone FN50
APC anti-human CD134 (OX40) antibody	BioLegend	BioLegend Cat# 350008;; RRID:AB_10719958, Clone Ber-ACT35 (ACT35)
PE anti-human CD274 (B7-H1, PD-L1) antibody	BioLegend	BioLegend Cat# 329706; RRID:AB_940368, Clone 29E.2A3
PE/Dazzle 594 anti-human CD154 antibody	BioLegend	BioLegend Cat# 310840; RRID:AB_2566245, Clone 24-31
Brilliant Violet 510 anti-human CD25 antibody	BioLegend	BioLegend Cat# 302640; RRID:AB_2629672, Clone BC96
BUV563 Mouse Anti-Human CD278	BD OptiBuild	BD Biosciences Cat# 741421, clone DX29
CD14 Monoclonal Antibody (61D3), APC-eFluor 780, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 47-0149-42; RRID:AB_1834358, Clone 61D3
CD16 Monoclonal Antibody (eBioCB16 (CB16)), APC-eFluor 780, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 47-0168-42; RRID:AB_11220086, Clone eBioCB16 (CB16)
CD20 Monoclonal Antibody (2H7), APC-eFluor 780, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 47-0209-42; RRID:AB_1272038, Clone 2H7
IL-13 Monoclonal Antibody (85BRD), FITC, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 11-7136-42; RRID:AB_2572515, Clone 85BRD
Alexa Fluor 700 anti-human IL-2 antibody	BioLegend	BioLegend Cat# 500320; RRID:AB_528929, Clone MQ1-17H12
PE/Dazzle 594 anti-human IL-10 antibody	BioLegend	BioLegend Cat# 506812; RRID:AB_2632783, Clone JES3-19F1
TNF alpha Monoclonal Antibody (MAb11), PE-Cyanine7, eBioscience	Thermo Fisher Scientific	Thermo Fisher Scientific Cat# 25-7349-82; RRID:AB_469686, Clone MAb11
Brilliant Violet 785 anti-human IL-17A antibody	BioLegend	BioLegend Cat# 512338; RRID:AB_2566765, Clone BL168
BUV737 Mouse Anti-Human IFN-g Clone 4S.B3	BD Biosciences	BD Biosciences Cat# 612845, Clone 4S.B3
Anti-Human IgG (gamma-chain specific)-Peroxidase antibody produced in goat	Sigma-Aldrich	Sigma-Aldrich Cat# A6029; RRID:AB_258272
Goat Anti-Human IgM Polyclonal Antibody, Horseradish Peroxidase Conjugated	Sigma-Aldrich	Sigma-Aldrich Cat# A6907; RRID:AB_258318
Human IgA Fd PAN (A1/2)	Hybridoma Reagent Laboratory	Hybridoma Reagent Laboratory HP6123-HRP
Mouse IgG1 anti-Human IgA Fd PAN (A1/2)	Hybridoma Reagent Laboratory	Hybridoma Reagent Laboratory Cat# HP6123-HRP
Polyclonal human sera	This study
Human polyclonal sera	This study
Bacterial and Virus Strains
SARS-CoV-2-nanoLuc virus (WA1 strain) in which ORF7 was replaced by nanoluciferase gene (nanoLuc) was generated by reverse genetics	Hou et al., 2020	GenBank: MT461671.1
Pseudotyped DG-luciferase (G∗DG-luciferase) rVSV	Kerafast	Kerafast Cat# EH1020-PM
rVSV-SARS-CoV-2	This study
Biological Samples
Healthy unexposed donor blood samples	UC San Diego Health
Convalescent COVID-19 donor blood samples	LJI Clinical Core	https://www.iedb.org/
Acute and convalescent COVID-19 donor blood samples	UC San Diego Health
Chemicals, Peptides, and Recombinant Proteins
Synthetic peptides	Synthetic biolmolecules (aka A&A)	http://syntheticbiomolecules.com
Electron Microscopy Sciences 16% Paraformaldehyde Aqueous Solution, EM Grade, Ampoule 10 ML	Electron Microscopy Sciences	Electron Microscopy Sciences Cat# 15710
Thermo Scientific Hoechst 33342 Solution (20 mM)	Thermo Scientific	Thermo Scientific Cat# 62249
Mirus Bio TransIT-LT1 Transfection Reagent	Mirus Bio	Mirus Bio Cat# MIR 2304
recombinant SARS-CoV-2 Spike protein	This study
recombinant SARS-CoV-2 Spike protein receptor binding domain (RBD) protein	This study
Quick-RNA Viral Kit	Zymo Research	Zymo Research Cat # R1035, Lot # ZRC205587
TaqMan Fast Virus 1-Step Master Mix	Applied Biosystems	Applied BiosystemsCat # 4444434, Lot # 00900184
Critical Commercial Assays
CoronaCheckCOVID-19 Rapid Antibody Test Kit	20/20 BioResponse	https://coronachecktest.com/
Experimental Models: Cell Lines
Vero	ATCC	ATCC Cat# CCL-81, RRID:CVCL_0059
HEK293T	ATCC	ATCC Cat# CRL-3216, RRID:CVCL_0063
Oligonucleotides
nCOV_N1 Reverse Primer Aliquot	Integrated DNA Technologies	IDT Cat# 10006831, Lot #0000515800
nCOV_N1 Probe Aliquot	Integrated DNA Technologies	IDT Cat# 10006823, Lot #0000515803
2019-nCoV_N Positive Control	Integrated DNA Technologies	IDT Cat# 10006625, Lot #0000509951
nCOV_N1 Forward Primer Aliquot	Integrated DNA Technologies	IDT Cat# 10006830, Lot #0000515799
Recombinant DNA
phCMV3-SARS-CoV-2	This study; Spike cloned from synthetic, codon optimized DNA
Empty vector: phCMV3	Genlantis	Gelantis Cat# P003300
pCAGGS-VSV-G	Kerfast	Kerfast Cat# EH1017
Software and Algorithms
LEGENDplex v8.0	BioLegend	https://www.biolegend.com/
GraphPad Prism 8.4	GraphPad	https://www.graphpad.com/
FlowJo 10	FlowJo	https://www.flowjo.com/
IEDB	Grifoni et al., 2020a	https://www.iedb.org
corrplot package (v0.84) running under R (v3.6.1) in Rstudio(1.1.456)	Wei and Sikmo, 2017	https://github.com/taiyun/corrplot
Other
CellInsight CX5 High-Content Screening (HCS) Platform	Thermo Scientific	Thermo Scientific Cat# CX51110