REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-CD25-APC (PC61.5)	Thermo Fisher	Cat #17-0251-82; RRID: AB_469366
anti-CD8-Alexaflor488 (53-6.7)	Thermo Fisher	Cat #53-0081-82; RRID: AB_469897
anti-Vα2-E450 (B20.1)	Thermo Fisher	Cat #48-5812-82; RRID: AB_10804752
anti-Vβ5-PE (MR9-4)	BD Biosciences	Cat # 553190; RRID: AB_394698
anti-CD44-PerCp-Cyanine5.5 (IM7)	Thermo Fisher	Cat #45-0441-82; RRID: AB_925746
anti-CD69-PE-Cy7 (H1.2F3)	Thermo Fisher	Cat #25-0691-82; RRID: AB_469637
Anti-NP antibody	BioRad	Cat # MCA400; RRID: AB_2151884
m-IgGκ BP-HRP	Santa Cruz	Cat # sc-516102; RRID: AB_2687626
Bacterial and Virus Strains
A/Puerto Rico/8/34 (H1N1) (PR8)	de Wit et al., 2004	N/A
PR8; PB1-UFOΔ	This study	N/A
PR8; PB1-UFOSYN	This study	N/A
PR8; PB1-EXT+	This study	N/A
PR8; NP-EXTΔ	This study	N/A
PR8; NP-EXTSYN	This study	N/A
A/California/04/09(H1N1) (Cal09)	Ye et al., 2010	N/A
Cal09; PB1-UFOΔ	This study	N/A
Cal09; PB1-UFOSYN	This study	N/A
Cal09; PB2-UFOΔ	This study	N/A
Cal09; PB2-UFOSYN	This study	NA
Cal09; PA-UFOΔ	This study	NA
Cal09; PB1-UFOSYN	This study	NA
Cal09; HA-UFOΔ	This study	NA
Cal09; HA-UFOSYN	This study	NA
A/WSN/33(H1N1) (WSN)	Hoffmann et al., 2000	N/A
WSN; PB1-UFOΔ	This study	N/A
WSN; PB1-UFOSYN	This study	N/A
WSN; PB2-UFOΔ	This study	N/A
WSN; PB2-UFOSYN	This study	N/A
WSN; PA-UFOΔ	This study	N/A
WSN; PA-UFOSYN	This study	N/A
WSN; HA-UFOΔ	This study	N/A
WSN; HA-UFOSYN	This study	N/A
PB1-UFO(SIIN)	This study	N/A
NS-UFO(SIIN)	This study	N/A
PB1-SIIN	Wei et al., 2019	N/A
NA-SIIN	MRC-University of Glasgow Centre for Virus Research; As Bottermann et al., 2018	N/A
A/Udorn/72(H3N2)	The Roslin Institute, University of Edinburgh; As Clohisey et al., 2020	N/A
LASV (Josiah strain)	Department of Pathology, the University of Texas Medical Branch	N/A
B/Wisconsin/01/2010	Department of Microbiology, Icahn School of Medicine at Mount Sinai	N/A
Biological Samples
Primary CD14+ human monocytes	The Roslin Institute, University of Edinburgh; As Clohisey et al., 2020	N/A
Chemicals, Peptides, and Recombinant Proteins
Dulbecco’s Modified Eagle Medium (DMEM)	Thermo Fisher / GIBCO	Cat#11965175
Minimum Essential Medium (MEM)	Sigma-Aldrich	Cat# 51411C
Purified Agar	Oxoid	Cat #: LP0028
Trypsin from bovine pancreas, TPCK-treated	Sigma-Aldrich	Cat #: T1426-500MG
Protease Inhibitor Cocktail Set III, EDTA-Free - Calbiochem	EMD Millipore	Cat# 539134-10ML
Trypsin	Sigma-Aldrich	Cat# T8802-100MG
TRIzol Reagent	Thermo Fisher Scientific	Cat#15596018
SimplyBlueTM SafeStain	Thermo Fisher Scientific	Cat# LC6060
NuPage 4−12% BT Gel 1.5mm 12w 10 Per Box	Thermo Fisher Scientific	Cat# NP0322BOX
MG-132	Sigma-Aldrich	Cat# M7449-1ML
NuPAGE MOPS SDS Running Buffer (20X)	Thermo Fisher Scientific	Cat# NP0001
Ovalbumin (257-264) chicken	Sigma-Aldrich	Cat# S7951
LT-1 transfection reagent	Mirius	Cat# MIR 2304
recombinant human colony-stimulating factor 1	A gift from Chiron, Emeryville, CA, US; As Clohisey et al., 2020	N/A
Lys-C lysyl endopeptidase	Wako	121-05063
Harringtonine	LKT biochemicals	H0169
Cycloheximide	Sigma-Aldrich	Cat# C7698
Sequencing grade modified trypsin	Promega	9PIV511
Critical Commercial Assays
Dual Luciferase Reporter Assay System	Promega	Cat#E1910
CD8a+ T Cell Isolation Kit	Miltenyi Biotec	Cat#130-104-075
EasySep Mouse CD8+ T Cell Isolation Kit	StemCell Technologies	Cat# 19853
PureLink RNA Mini Kit 250 Reactions	Thermo Fisher Scientific	Cat# 12183025
PureLink DNase Set	Thermo Fisher Scientific	Cat# 12185010
miRNeasy Mini Kit	QIAGEN	Cat# 217004
Q5 site directed mutagenesis kit	NEB	Cat# E0554S
Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat)	Illumina	Cat# MRZG12324
SMARTer total RNA Pico kit	Clontech	Cat# 634411
TruSeq Stranded Total RNA Library Prep Kit	Illumina	Cat # 20020596
Deposited Data
CAGE sequencing of WSN IAV virus infected cells	Clohisey et al., 2020	https://fantom.gsc.riken.jp/5/data/
DEFEND seq of PR8 IAV infected A549 cells	Rialdi et al., 2017	GEO: GSE96677
DEFEND seq of IBV infected A549 cells	This study	GEO: GSE85474
Ribosome Profiling of PR8 IAV infected cells	This study	GEO: GSE148245
CAGE sequencing of LASV infected vero cells	This study	GEO: GSE148122
RNA seq of PR8; PB1-UFOΔ and PR8;PB1-UFOSYN infected mouse lungs	This study	GEO: GSE128519
GISAID Database	Shu and McCauley, 2017	https://www.gisaid.org
NCBI Influenza Virus Database	Zhang et al., 2017	http://www.ncbi.nlm.nih.gov/genomes/FLU/Database
Mass spectrometry Data: PR8 IAV infected A549 and 293T cells	This study	Table S2A
Mass spectrometry Data: WSN IAV Virions	Hutchinson et al., 2014	https://massive.ucsd.edu/ProteoSAFe/datasets.jsp using the MassIVE ID MSV000078740; Table S2B
Mass spectrometry Data: Immunoprecipitation of PR8 IAV RdRp	Heaton et al., 2016	Table S2C
Experimental Models: Cell Lines
Dog: MDCK	ATCC	CCL-34; RRID: CVCL_0422
Human: A549	ATCC	CCL-185; RRID: CVCL_0023
Human: 293T	ATCC	CRL-3216; RRID: CVCL_0063
Cow: MDBK	Sigma	90050801-1VL; RRID: CVCL_0421
Monkey: Vero	ATCC	CCL-81; RRID: CVCL_0059
Mouse: DC2.4	Sigma-Aldrich	Cat# SCC142; RRID: CVCL_J409
Hamster: BSR-T7/5	Buchholz et al., 1999	N/A
Experimental Models: Organisms/Strains
Mouse: BALB/cJ (6-8 weeks)	Jackson Laboratories	00651
Chicken: Specific Pathogen Free Fertile Eggs	Charles River	Cat #: 10100329
Mouse: OT-I: C57BL/6-Tg(TcraTcrb)1100Mjb/J	The Jackson Laboratory / in-house; Hogquist et al., 1994	Cat# 003831; RRID: IMSR_JAX:003831
Mouse: C57BL/6 (10-14 weeks)	Envigo	N/A
Oligonucleotides
DEFEND-seq cDNA synthesis–3’ primer	Rialdi et al., 2017	N/A
qPCR Primers	This Study	Table S4B
Recombinant DNA
PR8 pDUAL plasmids	A kind gift of Prof Ron Fouchier; de Wit et al., 2004	N/A
Cal09 pDP2002 plasmids	A kind gift of Prof Daniel Perez.; Ye et al., 2010	N/A
pT7HRTMRen(-)	MRC-University of Glasgow Centre for Virus Research; Rezelj et al., 2019	N/A
pTMHRTN	MRC-University of Glasgow Centre for Virus Research; Rezelj et al., 2019	N/A
pTMHRTL	MRC-University of Glasgow Centre for Virus Research; Rezelj et al., 2019	N/A
pTM1-FFLuc	MRC-University of Glasgow Centre for Virus Research; Rezelj et al., 2019	N/A
pRL-TK	Promega	E2241
Software and Algorithms
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Bowtie	Langmead et al., 2009	http://bowtie-bio.sourceforge.net/index.shtml
MaxQuant	Cox and Mann, 2008	https://www.biochem.mpg.de/5111795/maxquant
Cutadapt	Martin, 2011	https://cutadapt.readthedocs.io/en/stable/
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
FlowJo	Treestar	N/A
Metascape	Zhou et al., 2019	https://metascape.org/gp/index.html#/main/step1
Vienna RNA Webserver	Gruber et al., 2008	http://rna.tbi.univie.ac.at
FastTree	Price et al., 2010	http://www.microbesonline.org/fasttree
RAxML	Stamatakis, 2014	https://cme.h-its.org/exelixis/web/software/raxml/index.html
TreeTime	Sagulenko et al., 2018	https://github.com/neherlab/treetime
PANDASeq	Masella et al., 2012	https://github.com/neufeld/pandaseq
NetMHC (v3.4 and v4.0)	Andreatta and Nielsen, 2016	https://services.healthtech.dtu.dk/service.php?NetMHC-4.0
MUSCLE	Edgar, 2004	https://www.drive5.com/muscle/
HISAT2	Kim et al., 2015	http://daehwankimlab.github.io/hisat2
Prism 8	Graphpad	N/A