REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Immunofluorescence primary antibodies against N protein	Genetex	GTX135361; RRID:AB_2887484
Immunofluorescence primary antibodies against CD45	abcam	ab10558; RRID:AB_442810
Immunofluorescence secondary antibody	Jackson ImmunoResearch	715-606-151; RRID:AB_2340866
Immunofluorescence secondary antibody	Jackson ImmunoResearch	711-166-152; RRID:AB_2313568
DApI	Sigma	Cat# D9542
Mouse anti-CD11b-Pacific blue (clone M1/70)	ThermoFisher	RRID:AB_10372795
Mouse anti-CD11c-PE-Cy7 (clone N418)	BD Bioscience	RRID:AB_2870343
Mouse anti-Siglec-F-PE-CF594 (clone E50–2440)	BD Biosciences	RRID:AB_2687994
Mouse anti-F4/80-APC (clone BM8)	ThermoFisher	RRID:AB_469452
Mouse anti-Ly6C-FITC (clone HK1.4)	BD Bioscience	RRID:AB_394628
Mouse anti-Ly6G-PerCP-efluor710 (clone 1A8)	ThermoFisher	RRID:AB_2573893
Universal Innovex FcReceptor Blocker	Fisher	Cat# 50-486-803
Viability dye eF506	ThermoFisher	Cat# 65-0866-14
Hamster anti-Pan-leukocytes	Washington University Monoclonal Antibody Center	HAT13A
Hamster anti-T cells	Washington University Monoclonal Antibody Center	HAT19A
Hamster anti-B cells	Washington University Monoclonal Antibody Center	HASA7A
Hamster anti-CD18	Washington University Monoclonal Antibody Center	BAQ30A
Zenon Kit AF647	Invitrogen ThermoFisher Scientific	Z25208; RRID:AB_2736961
Zenon Kit AF488	Invitrogen ThermoFisher Scientific	Z25102; RRID:AB_2736942
Zenon Kit PE	Invitrogen ThermoFisher Scientific	Z25055; RRID:AB_2736983
Zenon Kit AF700	Invitrogen ThermoFisher Scientific	Z25011; RRID:AB_2736964
anti-CD11b-PE-Cy7	Novusbio	Cat# NB110-89474PECY7
anti-CD8b-BV650 (clone 341)	BD	Cat# 742918; RRID: AB_2741146
anti-CD4-BUV395 (clone GK1.5)	BD	Cat# 563790; RRID: AB_2738426
anti-MHCII-BV421 (clone 14-4-4S)	BD	Cat# 744830; RRID: AB_2742516
Bacterial and virus strains
Mycobacterium bovis BCG-TICE (TMC 1028)	ATCC	ATCC Number: 35743
SARS-CoV-2/SB2	Dr. Samira Mubareka, University of Toronto, ON, Canada	N/A
SARS-CoV-2/RIM-1	This study	GenBank accession number MW599736
Influenza A/Puerto Rico/8/34 (H1N1, PR8)	Dr. Jonathan A. McCullers (St. Jude Children Research Hospital)	N/A
Influenza A virus isolate A/H3N2 A/Hong-Kong/1/68	Dr. Salman Qureshi, McGill University, Montreal	N/A
Biological samples
LPS from E.coli O26:B6	Sigma	Cat# L2654
Chemicals, peptides, and recombinant proteins
Middlebrook 7H9 broth	Fisher Scientific	Cat# 271310
Glycerol	Wisent	Cat# 800-040-LL
Tween80	Fisher	Cat# 338-500; CAS Number 9005-65-6
BSA for ADC	Wisent	Cat# 800-195-EG
Dextrose for ADC	Fisher Scientific	Cat# D16-10; CAS Number 50-99-7
NaCl for ADC	Fisher Scientific	Cat# S6713
PBS	Gibco	Cat# 10-010-049
DMEM	Gibco	Cat# 11965-092
FBS	Gibco	Cat# 26140
Pen/Strep	Gibco	Cat# 15240062
10% Formalin	Sigma	HT501128-4L
Crystal violet (0.1% w/v in 10% EtOH)	Sigma	Cat# C0775; CAS Number 548-62-9
QIAzol Lysis Reagent	Qiagen	Cat# 79306
Chloroform	Sigma	Cat# 528730; CAS Number 67-66-3
1X EvaGreen qPCR mastermix	ABM	Cat# ABMMastermix-S
SYBR Select MasterMix	Applied Biosystems	Cat# 4472908
10mM Tris Base	Sigma	Cat# T1503-250G
1mM EDTA	Sigma	Cat# E7889-100ML
Tween 20	Sigma	Cat# P7949-500ML
DMSO	Sigma	Cat# D2438
TritonX	Sigma	Cat# T9284-500ML
donkey serum	Sigma	Cat# D9663-10ML
Bovine serum albumin	Cedarlane	Cat# AK8917-0500
DAKO	Cedarlane	Cat# S302380-2
DNAse	Stemcell	Cat# 7469
RPMI	Gibco	Cat# 11875119
HEPES	Wisent	Cat# 330-050-EL
Nonessential amino acids	Wisent	Cat# 321-010-EL
human Serum	Sigma	Cat# H4522-100ML
TPCK	Fisher	Cat# 20233
Collagenase IV	Sigma	Cat# C5138
Paraformaldehyde 16%	Thermo Fisher	Cat# 28908
Critical commercial assays
Viral DNA/RNA kit		N/A
QuantiTect Reverse Transcription Kit	ABM	Cat# 205311
Genezol TriRNA Pure Kit	Geneaid	Cat# GZX050
LunaScript RT SuperMix Kit	NEB	Cat# E3010L
2.5 HD Brown Detection Kit	Advanced Cell Diagnostics	Cat# 322300
Hamster IFN-β ELISA	MyBioSource	Cat# MBS014227
Hamster IL-6 ELISA	MyBioSource	Cat# MBS7606648
Deposited data
SARS-CoV-2/RIM-1 (formerly known as SARS-CoV-2/cp13.32, Lineage B.1.147)	GenBank	GenBank accession number MW599736
Experimental models: Cell lines
VeroE6 cells	ATCC	ATCC Number CRL-1586
MDCK cells	ATCC	ATCC Number CRL-2936
Experimental models: Organisms/strains
C57BL/6J mice	JAX	Cat# 000664
B6.Cg-Tg(K18-ACE2)2Prlmn/J mice	JAX	Cat# 034860
Syrian Golden Hamsters (Mesocricetus auratus)	Envigo	Cat# 089
Roborovski Hamsters (Phodopus roborovskii)	Breeder for Pet Shop Trade	N/A
Human PBMC	300BCG cohort between April 2017 and June 2018 at Radboud umc, Nijmegen, The Netherlands	N/A
Oligonucleotides
mouse hprt Fwd: 5′-aggacctctcgaagtgttgg-3′	IdT	N/A
mouse hprt Rev: 5′-aacttgcgctcatcttaggc-3′	IdT	N/A
mouse gapdh Fwd: 5′-ctgaggaccaggttgtctcc-3′	IdT	N/A
mouse gapdh Rev: 5′-ctccttggaggccatgtagg-3′	IdT	N/A
hamster gapdh Fwd: 5′-aaggccaacaccatcttcc-3′	IdT	N/A
hamster gapdh Rev: 5′-gaaggtgtggagatgatgacc-3′	IdT	N/A
viral SARS-CoV-2-RBD Fwd: 5′-CAATGGTTTAACAGGCACAGG-3′	IdT	N/A
viral SARS-CoV-2-RBD Rev: 5′-CTCAAGTGTCTGTGGATCACG-3′	IdT	N/A
viral SARS-CoV-2-UpE Fwd: 5′-attgttgatgagcctgaag-3′	IdT	N/A
viral SARS-CoV-2-UpE Rev: 5′-ttcgtactcatcagcttg-3′	IdT	N/A
IAV-PR8 NS1-Fwd: 5′-AGAAAGTGGVAGGCCCTCTTTGTA-3′	IdT	N/A
IAV-PR8 NS1-Rev: 5′-GGGCACGGTGAGCGTGAACA-3′	IdT	N/A
viral SARS-CoV-2-N2 primers were purchased from IdT as commercial 2019-nCoV_N2 Combined Primer/Probe Mix (Cat #RV202002 and #RV202016) as per In vitro Diagnostic Guideline by CDC (Catalog # 2019-nCoVEUA-01, Date 3/30/2020, CDC-006-00019, Revision 03)	IdT	N/A
human Il1b-Fwd: TACATCAGCACCTCTCAAGCA	IdT	N/A
human Il1b-Rev: CCACATTCAGCACAGGACTCT	IdT	N/A
human Il8-Fwd: CTGCGCCAACACAGAAATTAT	IdT	N/A
human Il8-Rev: CATCTGGCAACCCTACAACAG	IdT	N/A
human Ifnb-Fwd: ATTGTCAGTGTCAGAAGCTCC	IdT	N/A
human Ifnb-Rev: CTCAGGGATGTCAAAGTTCCTC	IdT	N/A
human Ccl2-Fwd: TCCTCGCAACTTTGTGGTAG	IdT	N/A
human Ccl2-Rev: TTCAGTTCCAGGTCATACACG	IdT	N/A
human Tnfa-Fwd: AGTGAAGTGCTGGCAACCAC	IdT	N/A
human Tnfa-Rev: GAGGAAGGCCTAAGGTCCAC	IdT	N/A
human Ifna-Fwd: TGGCTGTGAAGAAATACTTCCG	IdT	N/A
human Ifna-Rev: TGTTTTCATGTTGGACCAGATG	IdT	N/A
human Gapdh-Fwd: GGCTGTTGTCATACTTCTCATGG	IdT	N/A
human Gapdh-Rev: GGAGCGAGATCCCTCCAAAAT	IdT	N/A
Software and algorithms
GraphPad Prism v9.0.0	GraphPad	https://www.graphpad.com/scientific-software/prism/
FlowJo v10	BD	https://www.flowjo.com/solutions/flowjo/downloads
Aperio ImageScope	Leica	https://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescope/
ZEISS ZEN 2.3 Pro	Zeiss	https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html
ImageJ	NIH	https://imagej.net/software/fiji/