REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
BV421 anti-human CCR7 (clone G043H7)	BioLegend	Cat# 353208
BV711 anti-human CCR6 (clone G034E3)	BioLegend	Cat# 353436
BV750 anti-huamn CXCR5 (clone RF8B2)	BD Biosicences	Cat# 747111
BUV563 anti-huamn CCR5 (clone 2D7)	BD Biosicences	Cat# 741401
PE-Cyanine7 anti-human CXCR3 (clone CEW33D)	ThermoFisher	Cat# 25-1839-42
PerCP-eFluor710 anti-human TCR γδ (clone B1.1)	ThermoFisher	Cat# 46-9959-42
APC-Fire810 anti-human CD38 (clone HIT2)	BioLegend	Cat# 303549
FITC anti-human CD57 (clone HNK-1)	BioLegend	Cat# 359604
PE-Cyanine5 anti-huamn CD95 (clone DX2)	ThermoFisher	Cat# 15-0959-42
Spark-NIR685 anti-huamn CD19 (clone H1B19)	BioLegend	Cat# 302270
Spark-NIR550 anti-human CD14 (clone 63D3)	BioLegend	Cat# 367148
PerCP anti-human CD45 (clone H130)	ThermoFisher	Cat# MHCD4531
PE anti-huamn CD25 (clone BC96)	ThermoFisher	Cat# 12-0259-42
APC anti-human CD27 (clone O323)	ThermoFisher	Cat# 17-0279-42
APC-eFluor780 anti-human HLA-DR (clone L243)	ThermoFisher	Cat# 47-9952-42
PerCP-Cyanine5.5 anti-human CD11b (clone ICRF44)	BioLegend	Cat# 301328
PE-eFluor610 anti-human CD24 (clone eBioSN3 (SN3 A5-2H10))	ThermoFisher	Cat# 61-0247-41
Alexa Fluor®647 anti-human CD1c (clone L161)	BioLegend	Cat# 331510
APC-R700 anti-human CD127 (clone HIL-7R-M21)	BD Biosicences	Cat# 565185
BUV496 anti-human CD16 (clone 3G8)	BD Biosicences	Cat# 612944
BV480 anti-human IgD (clone IA6-2)	BD Biosicences	Cat# 566138
BUV395 anti-human CD45RA (clone 5H9)	BD Biosicences	Cat# 740315
BUV737 anti-human CD56 (clone NCAM16.2)	BD Biosicences	Cat# 612766
BUV805 anti-human CD8 (clone SK1)	BD Biosicences	Cat# 612889
BUV661 anti-human CD11c (clone B-ly6)	BD Biosicences	Cat# 612967
SuperBright436 anti-human CD123 (clone 6H6)	ThermoFisher	Cat# 62-1239-42
BV570 anti-human IgM (clone MHM-88)	BioLegend	Cat# 314517
BV650 anti-human CD28 (clone CD28.2)	BioLegend	Cat# 302946
BB515 anti-human CD141 (clone 1A4)	BD Biosicences	Cat# 566017
eFluor450 anti-human CD161 (clone HP-3G10)	ThermoFisher	Cat# 48-1619-42
BV510 anti-human CD3 (clone OKT3)	BioLegend	Cat# 317332
Pacific Orange anti-human CD20 (clone HI47)	ThermoFisher	Cat# MHCD2030
BV605 anti-human IgG (clone G18-145)	BD Biosicences	Cat# 563246
BV785 anti-human PD-1 (clone EH12.2H7)	BioLegend	Cat# 329929
BUV615 anti-human CD4 (clone SK3)	BD Biosicences	Cat# 612987
Biological samples
Peripheral blood from healthy and COVID-19 related subjects	Duke University Health System	NA
Chemicals, peptides, and recombinant rroteins
Live/Dead UV Blue	ThermoFisher	Cat# L34962
Brilliant Stain Buffer Plus	BD Biosicences	Cat# 566385
Critical commercial assays
Dead Cell Removal Kit	Miltenyi Biotec	Cat# 130-090-101
Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v1	10x Genomics
Deposited data
BALF scRNA-seq data	Liao et al.37	GSE145926
NPS scRNA-seq data	Chua et al.38	https://figshare.com/articles/COVID-19_severity_correlates_with_airway_epithelium-immune_cell_interactions_identified_by_single-cell_analysis/12436517
Supplemental data	This study	https://dx.doi.org/10.17632/csc9p34d5t.1
scRNA-seq data of PBMCs	This study	GSE171555
Flow cytometry data of PBMCs	This study	https://flowrepository.org/id/FR-FCM-Z3WR
Software and algorithms
FlowJo version 10.6.1	Tree Star	https://www.flowjo.com/
Omiq	Omiq	https://www.omiq.ai/
Cell Ranger version 3.1.0	10x Genomics	https://www.10xgenomics.com/
Seurat v3 R package		https://satijalab.org/seurat/
CellPhone DB v2		https://www.cellphonedb.org/
Reactome pathway database		https://reactome.org/
GraphPad Prism version 8		https://www.graphpad.com/