REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-human HLA ABC (clone W6/32) labeled with APC fluorophore	Biolegend	Cat# 311410; RRID:AB_314879
Mouse monoclonal anti-human CD3 (clone OKT3)	Biolegend	Cat# 317302; RRID:AB_571927
Mouse monoclonal anti-human CD28 (clone CD28.2)	Biolegend	Cat# 302902; RRID:AB_314304
Mouse monoclonal anti-human CD8 (clone SK1) labeled with APC fluorophore	Biolegend	Cat# 980904; RRID:AB_2616624
Mouse monoclonal anti-human CD3 (clone SK7) labeled with PE-Cy7 fluorophore	Biolegend	Cat# 344816; RRID:AB_10640737
LIVE/DEAD Violet Viability	Life Technologies	Cat# L34960
CellTrace CFSE Cell Proliferation	Life Technologies	Cat# C34554
Biological samples
PBMC Specimens: Healthy Donors	Ragon Institute	N/A
PBMC Specimens: COVID-19 Patients	MassCPR	N/A
PBMC Specimens: mRNA Vaccine Recipients	MGH	N/A
Chemicals, peptides, and recombinant proteins
SARS-CoV-2 Networked Epitope Peptide Pools	MGH Peptide Core	N/A
PepMix Full SARS-CoV-2 Spike Peptide Pool	JPT	PM-WCPV-S
CEF Extended Peptide Pool	Mabtech	Cat# 3618-1
β2-Microglobulin	Sino Biological	Cat# 11976-H08H
Critical commercial assays
Human IFN-gamma ELISpot Basic Kit	MABTECH	Cat# 3420-2A
Human CD4 microbeads	Miltenyi Biotec	Cat# 130-045-101
Experimental models: Cell lines
Human: 721.221 cells + Cas9 + HLA + sgRNA TAP	Kaseke et al., 2021	N/A
Human: HEK293T cells	ATCC	N/A
Human: HEK293T-humanACE2 cells	A gift from Alex Balazs, Ragon Institute	N/A
Oligonucleotides
Primers for site-directed mutagenesis of HDM-SARS2-Spike-delta21, see Table S2	This paper	Table S2
Recombinant DNA
HDM-SARS2-Spike-delta21	Crawford et al., 2020	Addgene #155130
pHAGE-CMV-Luc2-IRES-ZsGreen-W	BEI	NR-52516
HDM-Hgpm2	BEI	NR-52517
HDM-tat1b	BEI	NR-52518
pRC-CMV-Rev1b	BEI	NR-52519
pHEF-VSVG	(Coleman et al., 2003)	Addgene #22501
Software and algorithms
Structure-based Network Analysis Pipeline	Gaiha et al., 2019	https://doi.org/10.5281/zenodo.2597484.