Reagent/Resource	Reference or Source	Identifier or catalog number
Experimental models
Vero CCL‐81	ATCC	CCL‐81
HEK293T	ATCC	CRL‐3216
L929	ATCC	CCL‐1
Vero ACE2/TMPRSS2	Papa et al (2021)	Vero ACE2/TMPRSS2
HEK293T ACE2	Papa et al (2021)	HEK293T ACE2
SARS‐CoV‐2/human/Liverpool/REMRQ0001/2020	Papa et al (2021)	Kind gift from Lance Turtle (University of Liverpool) and David Matthews and Andrew Davidson (University of Bristol)
MHV‐A59		Kind gift from Ian Goodfellow (Cambridge University)
Antibodies
MHV‐A59 polyclonal antiserum raised against disintegrated, purified MHV‐A59 virions (Rottier et al, 1981)	Dr. Peter Rottier (Utrecht University).	MHV‐A59 polyclonal antiserum
Monoclonal Anti‐Murine Coronavirus Nucleocapsid (N) Protein, Clone 1.16.1	BEI Resources, NIAID, NIH	NR‐45106
Mouse anti‐GFP antibody	Rockland	9F9.F9; 600‐301‐215
Rabbit anti‐N antibodies	Millipore	ABIN129544
Rabbit normal IgG	Millipore	12‐370
Rabbit anti‐TRIM21	Abcam	ab207728
Mouse TRIM21	Santa Cruz	sc‐21367
Rabbit anti‐Vinculin	Abcam	ab217171
Rabbit anti‐COX IV	LICOR	926‐42214
HRP‐coupled secondary anti‐mouse light chain specific	Millipore	AP200P
Anti‐rabbit light chain specific	Millipore	MAB201P
Anti‐SARS‐CoV‐2 S	Invitrogen	PA1‐41165
Anti‐IFN‐γ antibody 1‐D1K	Mabtech	cat#3420‐3
Anti‐biotin monoclonal antibody	Vector Labs	#SP‐3020
IgG‐A488	Molecular Probes	A11055
Oligonucleotides and other sequence‐based reagents
For long lists of oligos or other sequences please refer to the relevant Table(s) or EV Table(s)
CDC‐N2 (IDT 2019‐nCoV RUO kit)	CDC	143503
SARS‐CoV‐2_N_Positive control RNA	IDT	10006625
Chemicals, Enzymes and other reagents (e.g. drugs, peptides, recombinant proteins, dyes etc.)
Methylene blue	Sigma	M4159
Toluidine blue	Sigma	M4159
Formaldehyde	Sigma	T3260
ATPlite 1‐step luminescence reagent	Perkin Elmer	6016731
RIPA buffer	Cell Signalling Technology	CST‐9806
NuPAGE LDS Sample Buffer	Thermo Fisher	NP0007
NuPAGE 4–12% Bis‐Tris Gels	Thermo Fisher	NP0326BOX
Protease Inhibitor Cocktail	Roche	P8340
ECL Western Blotting Detection Reagent	Amersham	RPN2106
SARS‐CoV‐2 serology assay	Bio‐Techne	SA‐001
Separation module 12–240 kDa	Bio‐Techne	SM‐W004
RNAsecure	Invitrogen	AM7006
Luna® Universal Probe One‐Step	NEB	E3006
PepTivator SARS‐CoV‐2 protein N peptide pool	Miltenyi Biotec	130‐126‐698
Lymphoprep	StemCell	07801
ELISpot MAIP plates	Millipore	MAIPS4510
8‐well chambered coverslips	Ibidi	41122111
Cas9 protein	IDT	#1081060
Alt‐R Cas9 Electroporation Enhancer	IDT	#1075915
Software
Compass	Bio‐Techne	https://www.proteinsimple.com/compass/downloads/
Eclipse software	Sony
GraphPad Prism 9	GraphPad
Other
PMA‐Lite LED Photolysis blue light device	Generon	E90002
Jess capillary protein detection system	ProteinSimple
Neon Transfection System	Thermo Fisher	MPK5000
IncuCyte S3	Sartorius	IncuCyte S3
ABI StepOnePlus PCR System	Life Technologies
ELISpot reader	AID ispot, Autoimmun Diagnostika
Eclipse EC800 flow cytometer	Sony
Lumascope LS720 widefield microscope	Etaluma
PHERAstar FS plate reader	BMG