REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-SARS-CoV-2-NP	GeneTex	Cat# GTX135361; RRID: AB_2887484
Mouse anti-SARS-CoV-2-NP	Thermo Fisher	Cat# MA1-7403; RRID: AB_1018420
Mouse anti-SARS-CoV-2-SP	GeneTex	Cat# GTX632604; RRID: AB_2864418
Rabbit anti-ACE2	Abcam	Cat# ab15348; RRID: AB_301861
Mouse anti-TMPRSS2	Millipore-Sigma	Cat# MABF2158
Mouse anti-acetylated tubulin (ACTUB)	Santa Cruz	Cat# sc-23950 RRID:AB_628409
Mouse anti-MUC5AC	Abcam	Cat# ab212636
Rabbit anti-MUC1	Millipore-Sigma	Cat# HPA008855 RRID:AB_1846283
Rabbit anti-CX3CR1	Abcam	Cat# ab8021 RRID:AB_306203
Mouse anti-FOXJ1	Thermo Fisher	Cat# 14-9965-82 RRID:AB_1548835
Mouse anti-RSV	Millipore-Sigma	Cat# MAB858-1 RRID:AB_11203839
Mouse anti-PIV type 1	Novus Biologicals	Cat# NB100-63036 RRID:AB_964926
Mouse anti-PIV type 3	Novus Biologicals	Cat# MAB10207 RRID:AB_827567
Rabbit anti-EBP50	Thermo Fisher	Cat# PA1-090 RRID:AB_2191493
Mouse anti-EZR	Sigma-Aldrich	Cat# E8897 RRID:AB_476955
Rabbit anti-phospho-EZR	Cell Signaling	Cat# 3726T RRID:AB_10560513
Rabbit anti-SLK	Millipore-Sigma	Cat# HPA015757RRID:AB_1857236
Rabbit anti-SLK	Millipore-Sigma	Cat# HPA015757 RRID:AB_1857236
Rabbit anti-CEP164	Sigma-Aldrich	Cat# HPA037605 RRID:AB_10672908
Rabbit anti-IFT88	ProteinTech	Cat# 13967-1-AP RRID:AB_2121979
Mouse anti-ARL13B	NeuroMab	Cat# 75-287 RRID:AB_2341543
Rabbit anti-β-catenin	Thermo Fisher	Cat# AHO0462 RRID:AB_1500389
Rabbit anti-Phospho-PAK4	Cell Signaling	Cat# 3241S RRID:AB_2158623
Rabbit anti-PAK4	Cell Signaling	Cat# 62690S RRID:AB_2827508
Rabbit anti-Phospho-AKT	Abcam	Cat# ab192623
Rabbit anti- Phospho-Erk1/2	Cell Signaling	Cat# 9101S RRID:AB_331646
Mouse anti- Phospho-Erk1/2	Cell Signaling	Cat# 9107 RRID:AB_10695739
Rabbit anti-Phospho-p38	Cell Signaling	Cat# 4511T RRID:AB_2139682
Rabbit anti-BAIAP2	Millipore-Sigma	Cat# HPA027421 RRID:AB_10602392
Rabbit anti-PTPN14	Millipore-Sigma	Cat# HPA053864 RRID:AB_2682281
Rabbit anti-ARHGEF2	Millipore-Sigma	Cat# HPA043437 RRID:AB_2678481
Rabbit anti-MYH14	Millipore-Sigma	Cat# HPA067889 RRID:AB_2685917
Rabbit anti-CDK16	Millipore-Sigma	Cat# HPA001366 RRID:AB_1079584
Rabbit anti-PPP1R12A	Millipore-Sigma	Cat# HPA071956 RRID:AB_2732192
Rabbit anti-ANKRD35	Millipore-Sigma	Cat# HPA035453 RRID:AB_10672864
Rabbit anti-Phospho-JNK1/2	Cell Signaling	Cat# 4668T
Rabbit anti-Phospho-PAK1/2	Cell Signaling	Cat# 2601S PRID: AB_330220
Mouse anti-DM1α	Santa Cruz	Cat# sc-32293 RRID:AB_628412
Bacterial and virus strains
SARS-CoV-2 D614G	Joe De-Risi Lab, UCSF	SARS-CoV-2/human/USA/CA-UCSF-0001C/2020
SARS-CoV-2 BA.1	Melanie Ott Lab, UCSF	B.1.1.529 (California Department of Health)
SARS-CoV-2 BA.4	Melanie Ott Lab, UCSF	Clinical isolates
SARS-CoV-2 BA.5	Melanie Ott Lab, UCSF	Clinical isolates
Respiratory Syncytial Virus	Mark Peeples Lab, Rush-Presbyterian-St. Luke’s Medical Center	A2 strain
Parainfluenza Virus	Raymond Pickles Lab, University of North Carolina at Chapel Hill	JS strain
Biological samples
Human primary nasal epithelial cells	Jayakar Nayak lab and Carlos Milla Lab, Stanford University	Tables S1 and S2
K18-hACE2 mice	Jackson laboratory	034860
Chemicals, peptides, and recombinant proteins
DMSO	Sigma-Aldrich	Cat# 276855
Alexa Fluor™ Plus 647 Phalloidin	Invitrongen	A30107
DAPI	Bio Trend	Cat# 40043
Pen/Strep	Thermo Fisher	Cat# 15140163
Paraformaldehyde	AlfaAesar	Cat# 433689M
Normal Donkey Serum	Jackson ImmunoResearch	Cat# 017-000-121
NP40	Sigma	Cat# 11332473001
SiR-Tubulin	Cytoskeleton Inc.	Cat# CY-SC002
RBD protein	BPS Bioscience	Cat# 100688
Qdot™ 585 Streptavidin Conjugate	Thermo Fisher	Cat# Q10111MP
StcE	Carolyn Bertozzi Lab, Stanford University	NA
BSA	Sigma-Aldrich	Cat# A6003-25G
1X PBS	Corning	Cat# 46-013-CM
Triton X-100	USB	Cat# 22686
OCT compound	VWR	Cat# 25608-930
Saponin	Sigma-Aldrich	Cat# S7900
SARS-CoV-2 neutralizing antibody	Michael S. Diamond, Washington University in St. Louis	NA
Ciliobrevin D	Sigma-Aldrich	Cat# 250401
Camostat	Millipore-Sigma	Cat# SML0057
Hydroxychloroquine	Cayman	Cat# 17911
NSC-668394	Sigma-Aldrich	Cat# 341216
SB-633825	MCE	Cat# HY-108333
FRAX486	Cayman	Cat# 24682
LCH-7749944	MCE	Cat# HY-125035
KN-93	Cayman	Cat# 13319
MK-2206	Santa Cruz	Cat# sc-364537
Y27632	Santa Cruz	Cat# sc-281642A
MK2IV	Cayman	Cat# 14399
ARRY797	Biovision	Cat# B2462-5
Critical commercial assays
Adenylate kinase cytotoxicity bioassay	LONZA	Cat# LT17-217
In Situ Cell Death Detection Kit, TMR red	Sigma-Aldrich	Cat# 12156792910
TaqMan 2019-nCoV Control Kit v1	Thermo Fisher	Cat# A47533
RNAscope® Multiplex Fluorescent Reagent Kit v2	Bio-Techne	Cat# 323100
TSA Cyanine 3	Akoya Biosciences	Cat# NEL744001KT
High-Select Fe-NTA Phosphopeptide Enrichment Kit	Thermo Scientific	Cat# A32992
Deposited data
Phosphoproteome of SARS-CoV-2 infected Human Nasal Epithelium	This paper	PRIDE Project ID: PXD028123
Oligonucleotides
Human CEP83 shRNA	Dharmacon	Cat# SQ-20.0061
Non-Targeting Control Pool	Dharmacon	Cat# D-001910-10-50
Human EZR siRNA	Dharmacon	Cat# E−017370-00-0020
Human PAK4 siRNA	Dharmacon	Cat# E−003615-00-0020
ACE2 (Hs00222343_m1)	Life Technologies	Cat# 4331182
TMPRSS2 (Hs00237175_m1)	Life Technologies	Cat# 4331182
CX3CR1 (Hs01922583_s1).	Life Technologies	Cat# 4331182
Software and algorithms
ImageJ	NIH	https://imagej.nih.gov/ij/
Zen black	Carl Zeiss	https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html
GraphPad Prism 6	GraphPad	https://www.graphpad.com/