REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-CD3	Bio-Rad	MCA1477PB, CD3-12; RRID: AB_10843429
Anti-CD4	BioLegend	100451, GK1.5; RRID: AB_2564591
Anti-CD11b	Novus	NB110-89474, PECY7Poly; RRID: AB_1216361
Anti-RT1D	BioLegend	110211, 14-4-4S; RRID: AB_493214
Anti-CD3	Thermo-Fisher	RM-9107-S1; RRID: AB_149924
HRP-conjugated secondary IgG	Abcam	ab6892; RRID: AB_955427
HRP-conjugated secondary IgG	Brookwood BioMed	sab3003M
Bacterial and virus strains
Bacillus Calmette-Guérin (BCG)-Tice or OncoTICE	Merck	TICE® BCG
SARS-CoV-2 virus	CDC	Wuhan-1/2020
WA-1 (SARS-CoV-2/USA-WA1/2020 EPI_ISL_404895)	BEI Resources	NR-52281
Chemicals, peptides and recombinant proteins
SARS-CoV-2 N gene	Integrated DNA Technologies	10006625
Spike receptor-binding domain (S-RBD)	BEI Resources, NIAID	NR-52309
7H9 Middlebrook Medium	Fisher Scientific	B271310
OADC	Fisher Scientific	B11886
Glycerol	Sigma	G55116
Tween-80	Fisher Scientific	BP338
Minimum Essential Media (MEM)	Thermo Fisher	11095080
Fetal Bovine Serum (FBS)	Thermo Fisher	16140071
ACK lysis buffer	Thermo Fisher	A1049201
IC fixation buffer	eBiosciences	00-8222-49
RBC lysis solution	Miltenyi Biotec	130-094-183
Mouse lung dissociation kit	Miltenyi Biotec	130-095-927
Mouse spleen dissociation kit	Miltenyi Biotec	130-095-926
TRizol	Invitrogen	15596026
RNeasy kit	Qiagen	74004
TaqMan Fast Advanced Master Mix	Applied Biosystems	4444556
18F-FDG	SOFIE	F-18- fludeoxyglucose
Critical commercial assays
Zombie Aqua™ Fixable Viability Kit	Biolegend	423101
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)	10X Genomics	CG000315
UltraView DAB detection kit	Roche	05269806001
CellTiter-Glo® Luminescent Cell Viability Assay Kit	Promega	G9241
2019-nCoV CDC Research Use Only (RUO) kit	Integrated DNA Technologies	10006625
Deposited data
scRNA seq data	NCBI	GSE229135
Experimental models: Cell lines
Vero C1008 [Vero 76, clone E6] Cells: For vial growth, and vital stock preparation	American Type Culture Collection (ATCC)	ATCC CRL-1586
VeroE6-TMPRSS2 Cells: For determination of virus neutralization assay	Japanese Collection of Research Bioresources Cell Bank	JCRB1819
Experimental models: Organisms and strains
Male golden Syrian hamsters (Mesocrietus auratus), Strain HsdHan®: AURA	Envigo	HsdHan®:AURA
Software and algorithms
FACSDiva	BD	www.bdbiosciences.com
FlowJo (v10)	FlowJo	TreeStar
Cell Ranger v4.0.0	10X Genomics	www.10xgenomics.com
Seurat v4.0.4	(Hao et al., 2021)	github.com/satijalab/seurat
UCell	(Andreatta et al., 2021)	github.com/carmonalab/UCell
Metascape	(Zhou et al., 2019)	https://metascape.org
GraphPad Prism	Dotmatics, Prism - GraphPad	https://www.graphpad.com
Other
Animal bedding	Envigo	Teklad 7099 TEK-Fresh
Animal feed	Envigo	Teklad 2018 SX
GentleMACS Octo Dissociator with heaters	Mitenyi Biotec	130-096-427