REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monocolonal anti-SARS-CoV-2 nucleocapsid antibody	Sven Reiche, Friedrich Loeffler Institute, Riems, Germany	Cat#4E10A3A
Mouse monoclonal anti-SARS-CoV/SARS-CoV-2 (S2) antibody [1A9]	GenTex	Cat#GTX632604; RRID:AB_2864418
Goat anti-mouse IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 568	Thermo Fisher Scientific	Cat#A-11004; RRID:AB_2534072
Goat anti-mouse, horseradish peroxidase conjugated antibody	Merck	Cat#A9917; RRID:AB_258476
Bacterial and virus strains
Severe acute respiratory syndrome coronavirus 2	Wölfel et al., 2020	BavPat1/2020
Escherichia coli strain GS1783	(Tischer et al., 2010)	N/A
Biological samples
Hamster lungs, swabs, blood, intestines, kidneys	This paper	N/A
Chemicals, peptides, and recombinant proteins
high-fidelity polymerase PrimeSTAR GXL	Takara Bio	Cat#R050B
Xfect single shots transfection reagent	Takara Bio	Cat#631366
Avicel	FMC BioPolymer	N/A
Critical commercial assays
innuPREP Virus RNA Kit	Analytic Jena	Cat#845-KS-4700250
NEB Luna Universal Probe One-Step RT-qPCR kit	New England Biolabs	Cat#E3006L
Monarch DNA Gel Extraction Kit	New England Biolabs	Cat#T1020S
Monarch PCR & DNA Cleanup Kit	New England Biolabs	Cat#T1030S
mMESSAGE mMACHINE T7 transcription kit	Thermo Fisher Scientific	Cat#AM1344
Amersham ECL prime western blotting detection reagent	Thermo Fisher Scientific	Cat# RPN2236
Experimental models: Cell lines
African green monkey: Vero E6 cells	ATCC	Cat#CRL-1586
Hamster: BHK-21 [C-13]	ATCC	Cat#CCL-10
Saccharomyces cerevisiae: strain VL6-48N	Noskov et al., 2002	PMID: 11788734
Experimental models: Organisms/strains
model organism: Syrian hamster (Mesocricetus auratus)	Janvier Labs	RjHan:Aura
model organism: Roborovski dwarf hamster (Phodopus roborovskii)	German pet trade	N/A
Oligonucleotides
RT-qPCR primers and probe	Corman et al., 2020	N/A
Synthetic probes for the in situ-detection of the nucleocapsid RNA of SARS-CoV-2 (NCBI database NC_045512.2, nucleotides 28,274 to 29,533)	Thermo Fisher Scientific	assay ID: VPNKRHM
Recombinant DNA
synthetic reverse genetics platform of SARS-CoV-2	Thi Nhu Thao et al., 2020	N/A
Plasmid for expression of nucleocapsid of SARS-CoV-2 pVITRO2-EGFP-N	This paper	N/A
SARS-CoV-2 mutants containing recoded, codon pair deoptimized sequences	This paper	N/A
Deposited data
SARS-CoV-2 recoded, codon pair deoptimized sequences	GenBank	MZ064531 - MZ064546
Software and algorithms
GraphPad Prism, Version 8.4	GraphPad Software	https://www.graphpad.com
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
perl scripts for codon pair deoptimization	Kunec and Osterrieder, 2016	N/A