REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Human SARS Coronavirus Nucleoprotein/NP Monoclonal Antibody, Clone R040 1:1500	Sino Biological	REF 40143-R040 Lot MA14AP2104; RRID:AB_2827976
Anti-Iba1 Rabbit Polyclonal 1:4000	Wako Pure Chemical Corporation	REF 019-19741 Lot CAE1308; RRID:AB_839504
Anti-Human Myeloperoxidase, Polyclonal 1:1500	Dako	REF A0398 Lot 41321498; RRID:AB_2335676
Bacterial and virus strains
SARS-CoV-2	BEI Repository	Isolate: USA-WA1/2020
SARS-CoV-2	BEI Repository	Isolate: B.1.351
SARS-CoV-2	BEI Repository	Isolate: B.1.1.529
SARS-CoV-2	BEI Repository	Isolate: B.1.617.2
SARS-CoV-2	BEI Repository	B.1.1.7
Biological samples
Hamster SARS-CoV2 infected lung tissue, fixed, embedded	Bioqual, Inc.	N/A
Hamster SARS-CoV2 infected nasal turbinate, fixed, embedded	Bioqual, Inc.	N/A
Oral swabs from Hamster	Bioqual, Inc.	N/A
Chemicals, peptides, and recombinant proteins
Citrate buffer antigen retrieval	Thermo	AP-9003-500
Protein block	Biocare	BE965H
DaVinci Green Antibody diluent	Biocare	PD900M
Rabbit Mach-2 HRP-Polymer	Biocare	RHRP520L
Critical commercial assays
RNAscope® 2.5 HD Detection Reagents-RED	Advanced Cell Diagnostics	Cat. No.322360
SARS-CoV-2, S gene probe	Advanced Cell Diagnostics	848561; V-CoV2019-S
DapB Negative control probe	Advanced Cell Diagnostics	310043
Experimental models: Organisms/strains
Syrian golden hamsters	Envigo	HsdHan:AURA https://www.envigo.com/model/hsdhan-aura
Oligonucleotides
Primer:sgLeadSARSCoV2-F Forward: CGAT CTCTTGTAGATCTGTTCTC	Wolfel et al., 2020	ThermoFisher Scientific:4448510
Primer: E_Sarbeco_R Reverse: ATATTGC AGCAGTACGCACACA	Wolfel et al., 2020	ThermoFisher Scientific:4448510
Probe:E_Sarbeco_P1 : VIC-ACACTAG CCATCCTTACTGCGCTTCG-MGBNFQ	Wolfel et al., 2020	ThermoFisher Scientific:4448510
Primer:2019-nCoV_N1 Forward: GACCC CAAAATCAGCGAAAT	CDC Research Use Only 2019-Novel Coronavirus (2019-nCoV) Real-time RT-PCR Primers and Probes	ThermoFisher Scientific:4448510
Primer:2019-nCoV_N1 Reverse: TCTGGT TACTGCCAGTTGAATCTG	CDC Research Use Only 2019-Novel Coronavirus (2019-nCoV) Real-time RT-PCR Primers and Probes	ThermoFisher Scientific:4448510
Probe:2019-nCoV_N1 FAM- ACCCCGCAT TACGTTTGGTGGACC-BHQ1	CDC Research Use Only 2019-Novel Coronavirus (2019-nCoV) Real-time RT-PCR Primers and Probes	ThermoFisher Scientific:4448510
Recombinant DNA
Plasmid: pcDNA3.1+. SARS-CoV-2 E gene subgenomic RNA (sgRNA)	This paper	N/A
Software and algorithms
QuantStudio Real-Time PCR Software v1.7.1	Life Technologies	https://www.thermofisher.com/us/en/home/global/forms/life-science/quantstudio-6-7-flex-software.html
GraphPad Prism 8.4.2	GraphPad software	https://www.graphpad.com/scientific-software/prism/
BioRender	BioRender	https://biorender.com/
Other
RNA Standard: SARS-CoV-2 E gene subgenomic RNA (sgRNA)	This paper	N/A
RNA Standard: SARS-CoV-2 N gene genomic RNA (gRNA)	This paper	N/A
AmpliCap-Max T7 High Yield Message Maker Kit	Cellscript	C-ACM04037
RNeasy 96 QIAcube HT Kit	Qiagen	74182
SuperScript VILO Master Mix	Invitrogen	Life Technologies: 11755500