REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE-Cy7 anti-human CD107a (H4A3)	BD Biosciences, UK	Cat#561348; RRID:AB_10644018
BV510 anti-human CD3 (UCHT1)	BD Biosciences, UK	Cat#563109; RRID:AB_2732053
BV421 anti-human CD8 (RPA-T8)	BD Biosciences, UK	Cat#562428; RRID:AB_11154035
PE anti-human TNFa (MAb11)	Thermo Fisher Scientific	Cat#12-7349-82; RRID:AB_466208
FITC anti-human IFNγ (45-15)	Miltenyi Biotec Ltd	Cat# 130-091-641; RRID:AB_244194
FITC anti-human CD4 (SK3&SK4)	BD Bioscience, UK	Cat#347413; RRID:AB_400297
FITC anti-human CD8 (SK1)	BD Bioscience, UK	Cat#347313; RRID:AB_400279
BV421 anti-human CD19 (HIB19)	Biolegend, UK	Cat#302234; RRID: AB_10897802
Chemicals, peptides, and recombinant proteins
Synthesized peptides	GenScript Biotech, Netherlands	NA
QRNAPRITF-B∗27:05 pentamer	Proimmune	Cat#4354
KTFPPTEPK-A∗03:01 pentamer	Proimmune	Cat#4356A
MEVTPSGTWL-B∗40:01 pentamer	Proimmune	Cat#4328
FTSDYYQLY-A∗0101 pentamer	Proimmune	Cat#4355
KTFPPTEPK-A∗11:01 pentamer	Proimmune	Cat#4356B
NLLLQYGSFCTQLNR-DRA∗01:01/DRB1∗15:01 tetramer	Proimmune	NA (Custom)
IL-2/TCGF	Helvetica healthcare	Cat#0801017
IL-7	Biotechne, UK	Cat#207-IL
Critical commercial assays
Human IFN-γ ELISpot BASIC kit	Mabtech	Cat#3420-2A
SMARTer® RACE 5’/3′ kit	TaKaRa	Cat#634858
Monarch DNA gel extraction kit	New England BioLabs	Cat#T1020S
TOPO™ TA Cloning™ kit for sequencing	Thermo Fisher Scientific	Cat#K457501
RNeasy plus mini kit	Qiagen	Cat#74134
Advantage2 PCR kit	TaKaRa	Cat#639207
LIVE/DEAD fixable near-IR dead cell stain kit	Thermo Fisher Scientific	Cat#L34975
CellTrace™ CFSE cell proliferation kit	Thermo Fisher Scientific	Cat#C34554
CellTrace™ violet cell proliferation kit	Thermo Fisher Scientific	Cat#C34557
eBioscience™ 7-AAD viability staining solution	Thermo Fisher Scientific	Cat#00-6993-50
QIAprep spin miniprep kit	Qiagen	Cat#27106
Deposited data
GLUE mutation dataset – replacement (In supplementary information Mutation_identification, input_data)	CoV-GLUE	http://cov-glue.cvr.gla.ac.uk/#/home
GLUE mutation dataset – deletion (In supplementary information Mutation_identification, input_data)	CoV-GLUE	http://cov-glue.cvr.gla.ac.uk/#/home
COG-UK metadata (original data is unpublished and restricted by the data sharing agreement with COG-UK, data provided in supplementary information Tree_visualisation (input_data) has been cleaned for the purpose of public sharing and includes all publicly available variables required to recreate the analysis described)	COG-UK	https://www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Code for identifying mutation (In supplementary information Mutation_identification)	Custom	NA
Code for plotting variant prevalence (In supplementary information Variant_prevalence)	Custom	NA
Code for plotting global phylogenetic tree (In supplementary information Tree_visualisation)	Custom	NA
Experimental models: Cell lines
Lymphoblastoid cell lines (killing assay target cells) – transformed with epstein-Barr virus and ciclosporin A from healthy donors. Cell lines like this are a standard reagent in many laboratories. Cells are available upon request, contingent upon material transfer agreement and necessary ethical permissions.	Custom	NA
Oligonucleotides
Primer 5′-TGCTTCTGATGGCTCAAACAC AGCGACCT-3′	Custom	NA
Software and algorithms
Flowjo 10.7.1	BD Biosciences	NA
NetMHCpan 4.1	Reynisson et al. (2020)	http://www.cbs.dtu.dk/services/NetMHCpan/
R (version 3.5.3)	R Core Team, 2021	https://www.r-project.org
GraphPad prism 9	GraphPad	NA
Biorender	Science Suite inc	www.biorender.com
Other
FacsCanto II cytometer	BD Biosciences UK	NA