REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
HA.C5	Abcam	Cat #ab18181; RRID: AB_444303
Lamp1	Abcam	Cat #24170; RRID: AB_775978
Flag-M2	Sigma	Cat# SLBT7654; RRID: AB_259529
β-Actin	Sigma	Cat# A5441; RRID: AB_476744
HA.11	Biolegend	Cat# 902302; RRID: AB_2565019
p44/42 MAPK (Erk1/2)	Cell Signaling	Cat# 9102; RRID: AB_330744
Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204)	Cell Signaling	Cat# 4370; RRID: AB_2315112
Flag (DYKDDDDK Tag D6W5B)	Cell Signaling	Cat# 2368S; RRID: AB_2572291
ZO-1A12	ThermoFisher Scientific	Cat# 33-9100; RRID: AB_2533147
Chemicals, peptides, and recombinant proteins
TransIT-LT1	Mirus Bio	Cat# MIR2305
Cycloheximide	EMD Millipore	Cat# AC357420010
Fluorimount G	Southern Biotech	Cat# 0100-01
Hoechst 33342	ThermoFisher Scientific	Cat# 62249
TRIzol™ Reagent	ThermoFisher Scientific	Cat# 15596026
Dulbecco’s Modified Eagle’s (DMEM) complete medium	Corning	Cat# 10-017-CV
Fetal bovine serum (FBS)	Seradigm	Cat# 1500-500GH
Penicillin-streptomycin	Millipore Sigma	Cat# P4333-100ML
Paraformaldehyde	Electron Microscopy Sciences	Cat# 15710
Amersham ECL Western Blotting Detection Reagent	FisherScientific	Cat# 45-002-401
Deposited data
HEK 293T RNA-seq	This paper	NCBI under BioProject ID PRJNA767890 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA767890
Experimental models: Cell lines
HEK-293T (293T is an epithelial-like cell that was originally isolated from the kidney of a patient, age:fetus; available through ATCC)	ATCC	Cat# CRL-3216™; RRID: CVCL_0063
HeLa (Originally isolated in 1951 from a cervical carcinoma derived from a 31-year-old black female patient; available through ATCC)	ATCC	Cat# CCL-2™; RRID: CVCL_0030
Vero-E6 also known as Vero C1008 (African Green Monkey Kidney Cells with epithelial morphology; available through ATCC)	A generous gift from Carmen Foster at the Oak Ridge National Laboratory.	Cat# CRL-1586™; RRID: CVCL_0574
Recombinant DNA
N-terminal tagged HA-NRP1 and different mutants of HA-NRP1	GenScript (customized)
C-terminal tagged Flag-Plexin-A1	GenScript (customized)
N-terminal tagged Flag-SARS-CoV-2-S-original (NC_045512.2), Flag-SARS-CoV-2-B.1.1.7-S, Flag-SARS-CoV-B.1.351-S	GenScript (customized)
N-terminal tagged Flag-SARS-CoV-2-S1493−685	GenScript (customized)
Software and algorithms
GraphPad Prism v8	GraphPad	https://www.graphpad.com/
ImageJ	ImageJ software	https://imagej.net/Fiji
DESeq2	Bioconductor software	https://bioconductor.org/ https://bioconductor.org/packages/release/bioc/html/DESeq2.html