REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD71 M-A712 BV421	BD Biosciences	Cat#562995; RRID: AB_2737939
CD4 SK3 BV650	BD Biosciences	Cat#563875; RRID: AB_2744425
CD27 L128 BV711	BD Biosciences	Cat#563167; RRID: AB_2738042
CD38 HIT2 BV786	BD Biosciences	Cat#563964; RRID: AB_2738515
CCR7 150503 AF700	BD Biosciences	Cat#561143; RRID: AB_10562031
CD14 MΦP9 APC-H7	BD Biosciences	Cat#560180; RRID: AB_1645464
CD19 SJ25C1 APC-H7	BD Biosciences	Cat#560177; RRID: AB_1645470
CD45RA HI100 FITC	BD Biosciences	Cat#555488; RRID: AB_395879
CD8a SK1 PerCP-Cy5.5	BD PharMingen	Cat#565310; RRID: AB_2687497
CD95 DX2 PE-CF594	BD Biosciences	Cat#562395; RRID: AB_11153666
PD-1 EH12.1 PE-Cy7	BD Biosciences	Cat#561272; RRID: AB_10611585
CD3 OKT3 BV510	BioLegend	Cat#317332; RRID: AB_2561943
HLA-DR L243 BV605	BioLegend	Cat#307640; RRID: AB_2561913
CD69 FN50 BV421	BioLegend	Cat#310930; RRID: AB_2561909
CD103 Ber-ACT8 FITC	BioLegend	Cat#350203; RRID: AB_10642828
CD45RO UCHL1 PE-Cy7	Thermo Fisher Scientific	Cat#25-0457-41; RRID: AB_10717670
CD56 MEM-188 APC	BioLegend	Cat#304610; RRID: AB_314452
CD16 3G8 AF700	BioLegend	Cat#302026; RRID: AB_2278418
CD19 HIB19 BV570	BioLegend	Cat#302236; RRID: AB_2563606
CD3 UCHT1 PECF594	BD Biosciences	Cat#562280; RRID: AB_11153674
CD8a RPA-T8 BV421	BioLegend	Cat#301036; RRID: AB_10960142
Granzyme B GB11 AF700	BD Biosciences	Cat#560213; RRID: AB_1645453
Granzyme K G3H69 PerCP-eFluor710	Thermo Fisher Scientific	Cat#46-8897-42; RRID: AB_2573854
Granzyme M 4B2G4 eFluor660	Thermo Fisher Scientific	Cat#50-9774-42; RRID: AB_2574374
Perforin B-D48 Pe-Cy7	BioLegend	Cat#353316; RRID: AB_2571973
CD19 J4.119 ECD	Beckman Coulter	Cat#IM2708U; RRID: AB_130854
IgM G20-127 BUV395	BD Biosciences	Cat#563903; RRID: AB_2721269
CD21 B-ly4 BUV737	BD Biosciences	Cat#564437; RRID: AB_2738807
IgD IA6-2 PE-Cy7	BD Biosciences	Cat#561314; RRID: AB_10642457
IgG G18-145 BV786	BD Biosciences	Cat#564230; RRID: AB_2738684
Streptavidin BV510	BD Biosciences	Cat#563261; RRID: AB_2869477
CD20 2H7 APC-Cy7	BioLegend	Cat#302314; RRID: AB_314262
CD14 M5E2 BV510	BioLegend	Cat#301841; RRID: AB_2561379
CD8a RPA-T8 BV510	BioLegend	Cat#301048; RRID: AB_2561942
CD16 3G8 BV510	BioLegend	Cat#302048; RRID: AB_2562085
CD10 HI10a BV510	BioLegend	Cat#312220; RRID: AB_2563835
CD27 O323 BV605	BioLegend	Cat#302829; RRID: AB_11204431
IFN-γ RUO V450	BD Bioscience	Cat#560371; RRID: AB_1645594
TNF Mab11 AF700	BD Bioscience	Cat#557996; RRID: AB_396978
MIP-1b D21-1351 APC	BD Bioscience	Cat#560686; RRID: AB_1727565
CD107a eBioH4A3 ΩAF48	Thermo Fisher Scientific	Cat#53-1079-42; RRID: AB_2016657
Streptavidin PE	BD Biosciences	Cat#349023, RRID: AB_2868860
Streptavidin APC	BD Biosciences	Cat#349024, RRID: AB_2868861
Streptavidin PE	Thermo Fisher Scientific	Cat#S866
APC Conjugation Lightning-Link Kit	Abcam	Cat#ab201807
Peroxidase AffiniPure goat anti-human IgG, Fcγ fragment specific	Jackson ImmunoResearch	Cat#109-035-098; RRID: AB_2337586
Rat anti-human IgA mAb MT20, alkaline phosphate-conjugated	MabTech	Cat#3860-9A; RRID: AB_10736550
anti-human IgM mAb MT22, biotinylated	MabTech	Cat#3880-6-250
Bacterial and Virus Strains
SARS-CoV-2 isolate CoV/Australia/VIC01/2020	Caly et al., 2020	N/A
Biological Samples
Blood samples (peripheral blood mononuclear cells (PBMCs), serum and plasma samples) from COVID-19 patients and healthy control individuals	Alfred Hospital, Austin Health, The University of Melbourne, James Cook University, Australian Red Cross LifeBlood and Launceston General Hospital (Australia)	N/A
Tissue samples (tonsil, spleen and lung samples) from healthy control individuals	Launceston General Hospital, Alfred Hospital’s Lung Tissue Biobank and DonateLife Victoria (Australia)	N/A
Chemicals, Peptides, and Recombinant Proteins
AccuCheck Counting Beads	Thermo Fisher Scientific	Cat#PCB100
3,3¢,5,5¢-Tetramethylbenzidine (TMB) Liquid Substrate System for ELISA, peroxidase substrate	Sigma	Cat#T0440-1L
Alkaline phosphatase yellow (pNPP) liquid substrate for ELISA	Sigma	Cat#P7998-100ML
Pierce High Sensitivity Streptavidin-HRP	Thermo Fisher Scientific	Cat#21130
SARS-CoV-2 RBD protein	Amanat et al., 2020	N/A
SARS-CoV-2 RBD protein	Juno et al., 2020	N/A
SARS-CoV-2 Spike protein	Juno et al., 2020	N/A
PepTivator® SARS-CoV-2 Prot_S	Miltenyi Biotec	Cat#130-126-700
PepTivator® SARS-CoV-2 Prot_N	Miltenyi Biotec	Cat#130-126-698
PepTivator® SARS-CoV-2 Prot_M	Miltenyi Biotec	Cat#130-126-702
SARS-CoV-2 peptides - B7/N66-74 FPRGQGVPI; B7/N105-113 SPRWYFYYL; B7/N257-265 KPRQKRTAT; A2/N219-227 LALLLLDRL; A2/N222-230 LLLDRLNQL; A24/S1208 QYIKWPWYI	GenScript	N/A
HLA-B∗07:02 and HLA-A∗24:02 monomers with N105, N257, N66 (for HLA-B∗07:02) or S1208 (for HLA-A∗24:02) peptide	This paper	N/A
A2/S269 monomer (SARS-CoV-2, S269, YLQPRTFLL)	Habel et al., 2020	N/A
B7/EBV monomer (EBNA-3379-387, RPPIFIRRL)	Rowntree et al., 2020	N/A
Critical Commercial Assays
eBioscience™ Foxp3/Transcription Factor Staining Buffer Set	Thermo Fisher Scientific	Cat#00-5521-00
LEGENDplex™ Human Inflammation Panel 1 kit	BioLegend	Cat#740809
Experimental Models: Cell Lines
Vero C1008, African Green monkey kidney cells	ATCC	Cat#CRL-1586; Lot#3338237; RRID: CVCL_0574
Software and Algorithms
R v3.6.2	The Comprehensive R Archive Network	https://cran.r-project.org
Circlize R package	Gu et al., 2014	https://cran.r-project.org/package=circlize
ggplot R package	Wickham, 2016	https://ggplot2.tidyverse.org
TCRdist pipeline	Dash et al., 2017	https://github.com/phbradley/tcr-dist
lme4 R package	Bates et al., 2014	https://www.jstatsoft.org/article/view/v067i01/
FlowJo v10.5.3	FlowJo	https://www.flowjo.com
Prism v8.3.1 or v9.1.0	GraphPad	https://www.graphpad.com
BD FACS Diva v8.0.1	BD Biosciences	https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-software/flow-cytometry-acquisition/facsdiva-software
Other
Anti-PE MicroBeads	Miltenyi Biotec	Cat# 130-048-801, RRID: AB_244373
Anti-APC MicroBeads	Miltenyi Biotec	Cat# 130-090-855, RRID: AB_244367