REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
1G1 (PE) [anti-CCR4]	BD Biosciences	551120 (RRID:AB_394054)
11A9 (PE-Cy7) [anti-CCR6]	BD Biosciences	560620 (RRID:AB_1727440)
RPA-T8 or UCHT1 (BUV805) [anti-CD3]	BD Biosciences	565515 (RRID:AB_2739277)
RPA-T8 (BUV395) [anti-CD8]	BD Biosciences	563795 (RRID:AB_2722501)
M-A251 (PE-Cy5) [anti-CD25]	BD Biosciences	560988 (RRID:AB_2033955)
CD28.2 (BUV563) [anti-CD28]	BD Biosciences	564438 (RRID:AB_2738808)
HIT2 (BUV496) [anti-CD38]	BD Biosciences	564657 (RRID:AB_2744376)
FN50 (BV750) [anti-CD69]	BD Biosciences	563835 (RRID:AB_2738442)
FN50 (BUV737) [anti-CD69]	BD Biosciences	564439 (RRID:AB_2722502)
DX2 (BB630) [anti-CD95]	BD Biosciences	Custom conjugate
H4A3 (PE-CF594) [anti-CD107a]	BD Biosciences	562628 (RRID:AB_2737686)
BNI3 (BB755) [anti-CTLA-4]	BD Biosciences	560938 (RRID:AB_2033942)
RF8B2 (APC-R700) [anti-CXCR5]	BD Biosciences	565191 (RRID:AB_2739103)
GB11 (BB790) [anti-granzyme B]	BD Biosciences	Custom conjugate
G46-6 (BUV615) [anti-HLA-DR]	BD Biosciences	565073 (RRID:AB_2722500)
MQ1-17H12 (APC-R700) [anti-IL-2]	BD Biosciences	565136 (RRID:AB_2739079)
B56 (BB660) [anti-Ki-67]	BD Biosciences	Custom conjugate
T47-530 (BUV661) [anti-LAG-3]	BD Biosciences	Custom conjugate
δG9 (BB700) [anti-perforin]	BD Biosciences	Custom conjugate
741182 (BUV737) [anti-TIGIT]	BD Biosciences	Custom conjugate
C1.7 (PE/Dazzle 594) [anti-2B4]	BioLegend	393506 (RRID:AB_2734464)
G043H7 (APC-Cy7) [anti-CCR7]	BioLegend	353211 (RRID:AB_10915272)
M5E2 (BV510) [anti-CD14]	BioLegend	301842 (RRID:AB_2561946)
HIB19 (BV510) [anti-CD19]	BioLegend	302242 (RRID:AB_2561668)
O323 (BV785) [anti-CD27]	BioLegend	302832 (RRID:AB_2562674)
A1 (BV711) [anti-CD39]	BioLegend	328227 (RRID:AB_2632893)
HI100 (BV421) [anti-CD45RA]	BioLegend	304129 (RRID:AB_10900421)
HI100 (BV570) [anti-CD45RA]	BioLegend	304131 (RRID:AB_10897946)
A019D5 (BV605) [anti-CD127]	BioLegend	351334 (RRID:AB_2562022)
G025H7 (AF647) [anti-CXCR3]	BioLegend	353712 (RRID:AB_10962948)
4S.B3 (BV785) [anti-IFN-γ]	BioLegend	502542 (RRID:AB_2563882)
EH12.2H7 (PE-Cy7) [anti-PD-1]	BioLegend	367415 (RRID:AB_2616743)
F38-2E2 (BV650) [anti-TIM-3]	BioLegend	345027 (RRID:AB_2565828)
Mab11 (BV650) [anti-TNF]	BioLegend	502937 (RRID:AB_2561355)
4B41 (BV421) [anti-4-1BB]	BioLegend	309820 (RRID:AB_2563830)
C63D9 (AF488) [anti-TCF1]	Cell Signaling	6444 (RRID:AB_2797627)
REA473 (A647) [anti-TOX]	Miltenyi Biotec	130-107-838 (RRID:AB_2654224)
S3.5 (PE-Cy5.5) [anti-CD4]	Thermo Fisher Scientific	MHCD0418 (RRID:AB_10376013)
eBio64DEC17 (PE) [anti-IL-17A]	Thermo Fisher Scientific	12-7179-42 (RRID:AB_1724136)
Purified anti-CD28/CD49d	BD Biosciences	347690 (RRID:AB_647457)
Ultra-LEAF OKT3 Purified [anti-CD3]	BioLegend	317326 (RRID: AB_11150592)
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit	Thermo Fisher Scientific	Cat#L34957
Biological Samples
Acute moderate blood samples	Karolinska Hospital	N/A
Acute severe blood samples	Karolinska Hospital	N/A
Mild convalescent blood samples	Karolinska Hospital	N/A
Severe convalescent blood samples	Karolinska Hospital	N/A
Exposed family member blood samples	Karolinska Hospital	N/A
2020 blood donor samples	Karolinska Universitetslaboratoriet	N/A
2019 blood donor samples	Karolinska Universitetslaboratoriet	N/A
Chemicals, Peptides, and Recombinant Proteins
Synthetic CMV peptides	Peptides & Elephants GmbH	https://www.peptides.de/
Synthetic EBV peptides	Peptides & Elephants GmbH	https://www.peptides.de/
Synthetic overlapping SARS-CoV-2 peptides (Prot_M, N, S)	Miltenyi Biotec	https://www.miltenyibiotec.com/SE-en/
Optimal SARS-CoV-2 peptides	Peptides & Elephants GmbH	https://www.peptides.de/
Foxp3/TF Staining Buffer Set	Invitrogen	Cat#00-5523-00
Staphylococcal Enterotoxin B (SEB)	Sigma-Aldrich	Cat#S4881
Brefeldin A	BioLegend	Cat#420601
BD GolgiStop (with Monensin)	BD Biosciences	Cat#554724
BCIP/NBT Substrate	Mabtech	Cat#3650-10
BL21(DE3)pLysS Competent Cells	Novagen	Cat#69451
Triton X-100 Buffer	Sigma-Aldrich	Cat#X100
8M Urea Buffer	Sigma-Aldrich	Cat#51457
Cysteamine	Sigma-Aldrich	Cat#M9768
D-(+)-Biotin	Sigma-Aldrich	Cat#2031
Critical Commercial Assays
iFLASH Anti-SARS-CoV-2 IgG Kit	YHLO	Cat#20210217
LIAISON SARS-CoV-2 ELISA IgG Kit	DiaSorin	Cat#311450
Human IFN-γ ELISpot Kit	Mabtech	Cat#3420-2A
BD Multitest 6-color TBNK reagent with BD Trucount tubes	BD Biosciences	Cat#337166
CellTrace Violet Cell Proliferation Kit	Thermo Fisher Scientific	Cat#C34571
Software and Algorithms
NetMHCpan EL 4.1	DTU Bioinformatics	http://www.cbs.dtu.dk/services/NetMHCpan-4.1/
FlowJo 10.6.1	FlowJo	https://www.flowjo.com/
UMAP plugin 2.2	FlowJo	https://www.flowjo.com/
GraphPad Prism 8.4.2	GraphPad Software	https://www.graphpad.com/
PhenoGraph 0.2.1	PhenoGraph	https://omictools.com/phenograph-tool
RStudio	RStudio	https://rstudio.com/
Python (scikit-learn 0.22.1)	Python	https://www.python.org/