REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-dsRNA	English & Scientific Consulting	Cat #J2
Mouse polyclonal anti-3Dpol	Oh et al., 2009	N/A
Mouse monoclonal anti-tubulin	Sigma-Aldrich	Cat# T9026
Rabbit polyclonal anti-eIF4GI	Bethyl Laboratories	Cat# A300-502A
Mouse monoclonal anti-mCherry	Invitrogen	Cat# MA5-32977
Donkey polyclonal anti-mouse-Cy5	Jackson ImmunoResearch	Cat# 715-175-151
Goat polyclonal anti-mouse IRDye680	LI-COR	Cat# 926-68070
Goat polyclonal anti-rabbit IRDye800	LI-COR	Cat# 926-32211
Virus strains
CVB3	Wessels et al., 2006	N/A
EMCV	Duke and Palmenberg, 1989	N/A
eGFP-CVB3	Lanke et al., 2009	N/A
SunTag-EMCV	This study	N/A
SunTag-CVB3	This study	N/A
SunTag-CVB3Sabin-like1	This study	N/A
SunTag-CVB3Sabin-like2	This study	N/A
SunTag-CVB3Sabin-like3	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
DMEM	GIBCO	Cat# 31966021
Leibovitz’s L15 medium	GIBCO	Cat# 21083-027
Opti-MEM	Sigma-Aldrich	Cat# 11058-021
Methionine-free DMEM	GIBCO	Cat# 21013024
Advanced DMEM/F12	Thermo Fisher scientific	Cat# 12634-010
TryplE	Thermo Fisher scientific	Cat# 12605010
Fetal Bovine Serum (FBS)	Sigma-Aldrich	Cat# F7524
Penicillin-Streptomycin	GIBCO	Cat# 15140-122
Glutamine	Sigma-Aldrich	Cat# G6392-1VL
Cysteine	Sigma-Aldrich	Cat# C7352-10MG
FuGENE 6	Promega	Cat# E231A
Lipofectamine 2000	ThermoFisher	Cat #11668019
Lipofectamine RNAiMAX	Invitrogen	Cat# 13778-075
Polyethylenimine	Polysciences Inc	Cat# 23966
Polybrene	Santa Cruz Biotechnology, Inc	Cat# sc-134220
Propidium Iodide	Sigma-Aldrich	Cat# P4170
Doxycycline	Sigma-Aldrich	Cat# D9891-1G
Zeozin	Invitrogen	Cat# R25001
Puromycin	ThermoFisher Scientific	Cat# 12122530
Harringtonine	Cayman Chemical	Cat# 15361
GPC-N114	van der Linden et al., 2015	N/A
Rupitrivir	Sigma-Aldrich	Cat# PZ0315
Interferon α2	Sigma-Aldrich	Cat# IF007
scFv-sfGFP-StrepII	This study	N/A
Glucose oxidase	Sigma-Aldrich	Cat# G2133-10KU
Catalase	Sigma-Aldrich	Cat# C3515-10MG
Cultrex Basement Membrane Extract (BME), Growth Factor Reduced, Type 2	R&D Systems, Bio-Techne	Cat# 3533-001-02
Protease inhibitor cocktail	Roche	Cat# 11697498001
Rho kinase inhibitor	Calbiochem	Cat# 555550
TRIsure	Bioline	Cat# 38033
Atto633-NHS	Atto-Tec	Cat# AD 633-31
Cy5-azide	Lumiprobe	Cat# A3030
Amino-11-ddUTP	Lumiprobe	Cat# 15040
L-Homopropargylglycine	Sigma-Aldrich	Cat# 900893-100MG
Desthiobiotin	IBA Life Science	Cat# 2-1000-001
Digitonine	Sigma-Aldrich	Cat# D141
Paraformaldehyde	Aurion	Cat# 15710
Formamide	ThermoFischer	Cat# AM9342
Critical commercial assays
T7 RiboMax	Promega	Cat# P1320
HiScribe	New England Biolabs	Cat# E2040S
Superscript III reverse transcriptase	Invitrogen	Cat# 18080093
Tetro reverse transcriptase	Bioline	Cat# BIO-65050
Terminal deoxynucleotidyl Transferase	ThermoFisher	Cat# EP0162
iQ SYBR Green SuperMix	Bio-Rad	Cat# 1708885
Nucleospin RNA	Macherey-Nagel	Cat# 740990.50
Zymo RNA cleanup	ZymoResearch	Cat# R2061
Deposited Data
Raw and analyzed RNA sequencing -/+ IFN	Gene expression omnibus https://www.ncbi.nlm.nih.gov/geo/	GEO: GSE159280
Raw data of imaging experiments	Mendeley data	https://doi.org/10.17632/9sxbk6cvn9.1
Experimental Models: Cell Lines
U2OS cells	Tanenbaum lab	Cat# HTB-96
A549 cells	Van Kuppeveld lab	Cat# CCL-185
BHK-21 cells	Van Kuppeveld lab	Cat# CCL-10
HeLa cells	Tanenbaum lab	Cat# CCL-2
RPE1 cells	Tanenbaum lab	Cat# CRL-4000
HEK293T cells	Tanenbaum lab & Van Kuppeveld lab	Cat# CRL-3216
Oligonucleotides
See Table S2 for all sequences of smFISH probes, siRNAs, or qPCR oligos	This study	N/A
Recombinant DNA
Plasmids used in this study	Tanenbaum lab	https://www.tanenbaumlab.org/tools
Software and Algorithms
ImageJ	NIH	https://imagej.nih.gov/ij/
Micromanager	Micro-Manager 1.4.22	https://micro-manager.org
NIS-Elements Imaging software	Nikon	https://www.microscope.healthcare.nikon.com/en_EU/products/software
Graphpad Prism 8	GraphPad Software Inc	https://www.graphpad.com:443/scientific-software/prism/
Other
StrepTactin Sepharose beads	IBA life sciences	Cat# 2-1201-002
Zeba desalting column	VWR	Cat# GE17-0851-01
96-well glass bottom imaging plates-(Matriplates)	Brooks Life Science Systems	Cat# MGB096-1-2-LG-L