REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Live/Dead Zombie aqua	Biolegend	Ref. 423102
FITC anti-CD3, monoclonal mouse, clone HIT3a	BD Biosciences	Ref. 555332
FITC anti-CD14, monoclonal mouse, clone TUK4	Miltenyi Biotec	Ref. 130113146
FITC anti-CD16, monoclonal mouse, clone NKP15	BD Bioscience	Ref. 335035
FITC anti-CD19, monoclonal mouse, clone H1B19	Biolegend	Ref. 302205
FITC anti-CD163, monoclonal mouse, clone GHI/61	BD Biosciences	Ref. 563697
FITC anti-CD56, monoclonal mouse, clone HCD56	Biolegend	Ref. 318304
PE-Cy7 anti CD11c, monoclonal mouse, clone Bu15	Biolegend	Ref. 337216
BV650 anti-CD123, monoclonal mouse, clone 6H6	Biolegend	Ref. 306020
APC-vio770 anti-CD2, monoclonal mouse, clone LT2	Miltenyi Biotec	Ref. 130100231
APC anti-CD5, monoclonal mouse, clone L17F12	BD Biosciences	Ref. 555355
PerCp-efluo710 anti-CD1c, monoclonal mouse, cloneL161	Invitrogen	Ref. 46001542
PE anti-CD141, monoclonal mouse, clone AD514H12	Miltenyi Biotec	Ref. 130113318
PE-Dazzle594 anti-CD88, monoclonal mouse, clone S5/1	Biolegend	Ref. 344318
PE anti-CD45RA, monoclonal mouse, clone HI100	BD Biosciences	Ref. 555489
BUV395 anti-CD4 mouse anti-human, clone RPA-T4	BD Biosciences	Ref. 564724
FITC anti-CD3, mouse IgG2aκ, clone BW264/56	Miltenyi Biotec	Ref. 130113128
APC anti-CCR7, recombinant human IgG1, clone REA108	Miltenyi Biotec	Ref. 130120460
BV711 anti-CD123, mouse anti-human	Biolegend	Ref. 306030
BUV737 anti-CD86, monoclonal mouse, clone 2331 (FUN-1)	BD Biosciences	Ref. 612784
PE anti-CD80, monoclonal mouse, clone L307.4	BD Biosciences	Ref. 557227
PE-Cy7 anti-PD-L1, monoclonal mouse, clone 10F.9G2	Biolegend	Ref. 374506
BUV395 anti-HLADR, monoclonal mouse, clone G46-6	BD Biosciences	Ref. 564040
FITC anti-CCR7, monoclonal mouse, clone 150503	BD Biosciences	Ref. 560548
APC anti-CD62L, monoclonal mouse, clone SK11	BD Biosciences	Ref. 4094868
FITC anti-PD-L1, monoclonal mouse, clone MIH1	BD Biosciences	Ref. 558065
PerCP-efluor anti-CD1c, monoclonal mouse, clone L161	Invitrogen	Ref. 46001542
AF700 anti-CD14, monoclonal mouse, clone M5E2	BD Biosciences	Ref. 561029
BV421 anti-CD16, monoclonal mouse, clone 3G8	BD Biosciences	Ref. 562874
BV650 anti-CD80, monoclonal mouse, clone 2D10	Biolegend	Ref. 305227
APC anti-IFN-α, monoclonal mouse, clone LT27:295	Miltenyi Biotec	Ref. 130092602
BUV395 anti-CD4, monoclonal mouse, clone RPA-T4	BD Biosciences	Ref. 564724
BV421 anti-PD1 monoclonal mouse, clone EH12.2H7	Biolegend	Ref. 329919
APC-Cy7 anti-CD25, monoclonal mouse, Clone M-A251	BD Biosciences	Ref. 557753
Mouse monoclonal SARS-CoV/SARS-CoV-2 Nucleocapsid	Sino Biological	Cat #40143-MM05
Alexa Fluor® 647 AffiniPure Donkey Anti-Mouse IgG (H+L)	Jackson ImmunoResearch	Cat #715-605-150
Bacterial and virus strains
SARS-CoV2 Alpha B220/95	Isolated in Saint-Louis Hospital (Paris, France)	ID: EPI_ISL_469284 (220_95)
SARS-CoV2-variant 21A/Delta (B.1.617.2)	Laboratory of Olivier Schwartz	ID: EPI_ISL_2029113
SARS-CoV2-variant Omicron Oμ100.1 p2d4 (Omicron BA.1)	Laboratory of Olivier Schwartz	ID: EPI_ISL _6794907
Biological samples
Cytopheretic rings of healthy donors	Etablissement Francais du sang (French blood bank), Paris, Institut de recherche Saint-Louis	N/A
Chemicals, peptides, and recombinant proteins
Lymphoprep	Proteogenix	Ref. 3824565
Gibco™ RPMI 1640 with GlutaMAX	Thermo Fisher Scientific	Ref. 12027599
MEM nonessential amino acid	Thermo Fisher Scientific	Ref. 11140050
Dulbecco Modified Eagle Medium (DMEM)	Thermo Fisher Scientific	Ref. 41966-029
Hepes buffer solution (1M)	Thermo Fisher Scientific	Ref.15630-056
Glutamax (100X)	Thermo Fischer	Ref. 35050-087
Sodium pyruvate	Thermo Fisher Scientific	Ref. 11360070
Gibco™ Pénicilline-streptomycine (10 000 U/ml)	Thermo Fisher Scientific	Ref. 11548876
TLR7/TLR8 agonist R848 (Resiquimod)	InvivoGen	Ref. tlrl-r848-1
X-VIVO 15 avec Gentamicine Phenol Red avec Transferrine humaine	Lonza	UGAP 4165338
Dynabeads™ Human T-Activator CD3/CD28	Thermo Fisher Scientific	Ref. 11131D
Inhibitor cocktail- 500x, LOT 2290850	Invitrogen	Ref. 00-4980-93
eBeads eBioscience™ UltraComp	Thermo Fisher Scientific	Ref. 01-2222-42
CellTrace™ Yellow Cell Proliferation Kit,	Invitrogen™	Ref. 15584394
32% Paraformaldehyde (formaldehyde) aqueous solution	Electron Microscopy Sciences	Cat #15714
RNAse H	New England BioLabs	Ref. M0297S
Critical commercial assays
Easysep human panDC pre-enrichment kit	StemCell technologies	Ref. 19251
EasySep human Naïve CD4+ T cell isolation Kit 2	StemCell technologies	Ref. 17555
Fixation permeabilization buffer eBioscience	Thermo Fisher Scientific	Ref. 88-8824-00
Human IL-12p70 Flex Set	BD Biosciences	Ref. 558283
Human IL-2 Flex Set	BD Biosciences	Ref. 558270
Human IFN-γ Flex Set	BD Biosciences	Ref. 558269
Human IL-10 Flex Set	BD Biosciences	Ref. 558274
Human IL-1β Flex Set	BD Biosciences	Ref. 558279
Human IL-17A Flex Set	BD Biosciences	Ref. 560383
Human TNF Flex Set	BD Biosciences	Ref. 558273
Human IL-6 Flex Set	BD Biosciences	Ref. 558276
Human IL-8 Flex Set	BD Biosciences	Ref. 558277
Human IFN-α Flex Set	BD Biosciences	Ref. 560379
Human IL-13 Flex Set	BD Biosciences	Ref. 558450
IFN-λ1,3 DuoSet ELISA	RD Systems	Ref. DY1598B05
IFN-β DuoSet ELISA	RD Systems	Ref. DY81405
Maxima First Strand cDNA Synthesis Kit	Thermo Fisher Scientific	Cat #K1671
RNeasy mini kit	Qiagen	Cat #74106
Power SYBRgreen PCR Master mix	Applied Biosystems	Ref. 4367659
Deposited data
RNA-seq raw and analysed data	This paper	GSE294888 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294888
Experimental models: Cell lines
Vero E6	ATCC	Cat #CRL-1586
Oligonucleotides
E_Sarbeco Forward primer ACA GGT ACG TTA ATA GTT AAT AGC GT	Corman et al.51	N/A
E_Sarbeco Reverse primer ATA TTG CAG CAG TAC GCA CAC A	Corman et al.51	N/A
QuantiTect RT-PCR Primer assay HS_GAPDH	Qiagen	QT01192646
Software and algorithms
FlowJo software (version 10.10)	BD Biosciences	https://flowjo.com/flowjo10/download
FCAP array software	BD Biosciences	https://www.bdbiosciences.com/en-at/products/instruments/software-informatics/instrument-software/fcap-array-software-v3-0.652099?tab=product_details
Prism 9.5	GraphPad	https://www.graphpad.com/updates/prism-910-release-notes
Attune NxT software	Thermo Fisher Scientific	Version 2.6
R software	The Comprehensive R archive network	Version 4.3.2
pheatmap	Raivo Kolde	https://cran.r-project.org/web/packages/pheatmap/index.html
EnhancedVolcano	Kevin Blighe	https://github.com/kevinblighe/EnhancedVolcano
ComplexHeatmap	Zuguang Gu	https://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
ClusterProfiler	Guangchuang Yu, Li-Gen Wang	https://www.bioconductor.org/packages//2.13/bioc/html/clusterProfiler.html
Kallisto	Pachter laboratory	https://pachterlab.github.io/kallisto/
Tximport	Michael Love	https://www.bioconductor.org/packages/release/bioc/html/tximport.html
DESeq2	Michael Love	https://www.bioconductor.org/packages//2.13/bioc/html/DESeq2.html
GSVA	Robert Castelo	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
Other
LightCycler 480	Roche	N/A
Attune NxT	Thermo Fisher Scientific	N/A