REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
T7 Select 10-3b bacteriophage	EMD Millipore Sigma	Cat. #70014-3
Escherichia coli, strain BLT5403	EMD Millipore Sigma	Cat. # 70548-3
Biological samples
COVID-19 patient plasma and sera	This paper	See Tables 1 and S1
Healthy human sera	This paper	See Table 1
Endemic HCoV positive plasma and sera	This paper	See Table 1
Chemicals, peptides, and recombinant proteins
FuGENE-6	Promega	Cat. # E2692
Protein A Dynabeads	Thermo Fisher	Cat. # 10002D
Protein G Dynabeads	Thermo Fisher	Cat. # 10004D
Q5 High Fidelity 2X Master Mix	NEB	Cat. # M0492S
Critical commercial assays
QIAquick Gel Extraction Kit	QIAGEN	Cat. # 28704
AMPure XP	Beckman Coulter	Cat. # A63881
Quant-iT PicoGreen dsDNA Assay Kit	Thermo Fisher	Cat. # P7589
Bright-Glo Luciferase Assay System	Promega	Cat. # E2620
Deposited data
Demultiplexed Illumina sequencing reads	This paper	SRA: PRJNA72462
Experimental models: Cell lines
Human Embryonic Kidney (HEK293T)	ATCC	Cat. # CRL-11268
Human Embryonic Kidney cells expressing human ACE2 (HEK293T-hACE2)	BEI Resources	Cat. # NR-52511
Oligonucleotides
Oligonucleotide library FWD primer: 5′ AATGATACGGCAGGAATTCTACGCTGAGT 3′	Williams et al., 2019	N/A
Oligonucleotide library REV primer: 5′ CGATCAGCAGAGGCAAGCTTGCTATCA 3′	Williams et al., 2019	N/A
Illumina library prep primer, Round 1 FWD: 5′ TCGTCGGCAGCGTCTCCAGTCAGGTG TGATGCTC 3′	Williams et al., 2019	N/A
Illumina library prep primer, Round 2 REV: 5′ GTGGGCTCGGAGATGTGTATAAGAGAC AGCAAGACCCGTTTAGAGGCCC 3′	Williams et al., 2019	N/A
Illumina library prep primer, Round 2 FWD: 5′ AATGATACGGCGACCACCGAGATCTAC ACNNNNNNNNTCGTCGGCAGCGTCTCCAGTC 3′	Williams et al., 2019	N/A
Illumina library prep primer, Round 2 REV: 5′ CAAGCAGAAGACGGCATACGAGATNNN NNNNNGTCTCGTGGGCTCGGAGATGTGTA TAAGAGACAG 3′	Williams et al., 2019	N/A
Custom Illumina sequencing primer: 5′ GCT CGGGGATCCGAATTCTACGCTGAGT 3′	Williams et al., 2019	N/A
Recombinant DNA
HDM-SARS2-Spike-delta21 plasmid	Addgene	Cat. # 155130
Luciferase-IRES-ZsGreen plasmid	BEI Resources	Cat. # NR-52516
HDM-Hgpm2 gag/pol lentiviral helper plasmid	BEI Resources	Cat. # NR-52517
pRC-CMV-Rev1b plasmid	BEI Resources	Cat. # NR-52519
HDM-tat1b plasmid	BEI Resources	Cat. # NR-52518
Software and algorithms
Geneious R11	https://www.geneious.com	N/A
Prism 9	https://www.graphpad.com	N/A
Nextflow	Di Tommaso et al., 2017	https://github.com/matsengrp/pan-CoV-manuscript
Bowtie	Langmead et al., 2009	N/A
samtools-idxstats	Li et al., 2009	N/A
xarray	Hamman and Hoyer, 2017	N/A
phip-stat	Laserson Lab	https://github.com/lasersonlab/phip-stat
scipy.optimize	Virtanen et al., 2020	N/A
pairwise2	Cock et al., 2009	N/A
RStudio	https://www.rstudio.com	N/A