REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Polyclonal human sera	This study	N/A
Bacterial and Virus Strains
VSV-ΔG-GFP	Karafast	Cat# EH1020
rVSV-SARS-CoV-2	This study	N/A
rVSV-SARS-CoV-2 – D614G	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
Fugene 6	Promega	Cat# E2692
TransIT-LT1	Mirus	Cat# MIR 2304
PFA	Electron Microscopy Sciences	Cat# 15710
Hoechst	ThermoFisher Scientific	Cat# 62249
SuperScript IV (50rxn	ThermoFisher Scientific	Cat# 18090050
dNTP mix (10mM each)	ThermoFisher Scientific	Cat# R0192
Random hexamers (50uM)	ThermoFisher Scientific	Cat# N8080127
RNase OUT	ThermoFisher Scientific	Cat# 10777019
Q5 High-fidelity polymerase	New England Biolabs	Cat# M0491S
Critical Commercial Assays
Promega Luciferase Assay System	Promega	Cat# E1501
Britelite Plus Reporter Gene Assay System	Perkin-Elmer Part	Cat# 6066769
MagnaPure96 extraction platform	Roche Diagnostics Ltd, Burgess Hill, UK	Cat# 06 543 588 001
SensiFASTTM Probe No-ROX One-Step Real-time PCR kit	Bioline	Cat# BIO-76001
Ligation sequencing kit	Oxford Nanopore	Cat# SQK-LSK109
Native barcoding expansion kit 13-24	Oxford Nanopore	Cat# EXP-NBD114
Native barcoding expansion kit1-12	Oxford Nanopore	Cat# EXP-NBD104
Flow cell priming kit	Oxford Nanopore	Cat# EXP-FLP002
Flow cells R9.4.1 48pk	Oxford Nanopore	Cat# FLO-MIN106D
Flow cell wash kit	Oxford Nanopore	Cat# EXP-WSH003
SFP Expansion kit	Oxford Nanopore	Cat# EXP-SFB001
Next Ultra II library prep kit (illumina)	New England Biolabs	Cat# E7645L
Quick ligation module	New England Biolabs	Cat# E6056L
HIV-1 p24 ELISA	Perkin-Elmer	Cat# NEK050B
Deposited Data
COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE)	Johns Hopkins University	https://github.com/CSSEGISandData/COVID-19/blob/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv
GISAID	Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017	https://www.gisaid.org
STAY-AT-HOME ORDERS IN EUROPE		https://www.sidley.com/-/media/uploads/stay-at-home-tracker_europe.pdf?la=en
Experimental Models: Cell Lines
HEK293T/17 cells	ATCC	Cat# CRL-11268
293T/ACE2.MF	Dr. Michael Farzan and Huihui Mu	N/A
TZM-bl/ACE2.MF	Dr. Michael Farzan and Huihui Mu	N/A
293T	ATCC	Cat# CRL-3216
Vero	ATCC	Cat# CCL-81
293T-Ace2	This study	N/A
293T-Ace2-TMPRSS2	This study	N/A
Oligonucleotides
Primer pool1 and Primer Pool2 for sequencing (98 oligonucleotides	Artic Network	https://artic.network/ncov-2019
Recombinant DNA
VRC7480 (Spike plasmid)	Drs. Barney Graham and Kizzmekia Corbett	N/A
VRC7480.D614G (Spike plasmid)	This study	N/A
pCMV ΔR8.2 (lentiviral backbone)	Drs. Barney Graham and Kizzmekia Corbett	N/A
pHR’ CMV Luc (luciferase reporter)	Drs. Barney Graham and Kizzmekia Corbett; Naldini et al., 1996	N/A
pSG3ΔEnv	Drs. Beatrice Hahn and Feng Gao	N/A
Empty vector: phCMV3	Genlantis	Cat# P003300
pCAGGS-VSV-G	Kerfast	Cat# EH1017
phCMV3-SARS-CoV-2	This study, Spike cloned from synthetic, codon optimized DNA	N/A
phCMV3-SARS-CoV-2 – D614G	This study, generated through site-directed mutagenesis	N/A
Software and Algorithms
R	The R Foundation for Statistical Computing	http://www.R-project.org
Nanopolish	© Ontario Institute for Cancer Research 2015 MPL liscense	https://github.com/jts/nanopolish
R packages: phangorn (version 2.5.5), ggplot2 (version 3.3.0), beeswarm (version 0.2.0), tidyverse (version 1.3.0), ape (version 5.3), lme4 (version 1.1.21)	The R Foundation for Statistical Computing	https://cran.r-project.org/
data.table (version 1.12.8)	Matt Dowle	https://github.com/Rdatatable/data.table
Aliview	Anders Larsson	https://ormbunkar.se/aliview/
cgam (version 1.14)	Xiyue Liao, Mary C. Meyer	https://www.jstatsoft.org/htaccess.php?volume=089&type=i&issue=05
ARTIC network protocol (accessed the 19th of April)	ARTIC network	https://artic.network/ncov-2019
Python Matplotlib A 2D Graphics Environment v 3.2.2	Hunter, 2007	https://matplotlib.org
The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC	Schrödinger	https://pymol.org/2/
Oblong	Goloboff, 2014	http://www.lillo.org.ar/phylogeny/oblong/
Los Alamos National Lab HIV Database: Analyze Align and Entropy	Los Alamos National Lab	http://cov.lanl.govcontent/index
Los Alamos National Lab SARS-CoV-2 Analysis Pipeline: SARS-CoV-2 map, Relative Frequency Change by Geographical Region, Rainbow Tree	This study	http://cov.lanl.govcontent/index
PAUP	David Swofford	https://paup.phylosolutions.com
GraphPad Prism 8	GraphPad Software, Inc	https://www.graphpad.com
Other
Published primers and probes for the SARS-CoV-2 E-gene RT- qPCR SARS-CoV-2	Corman et al., 2020	N/A
ABI Thermal Cycler	Applied Biosystems, Foster City, United States	Cat# 4375305
CellInsight CX5 High Content Screening Platform	ThermoFisher Scientific	Cat# CX51110