REAGENT or RESOURCE	SOURCE	IDENTIFIER
Media and buffers
DMEM media	Gibco	Cat#: 11966025
Opti-MEM I reduced serum media	Gibco	Cat#: 15392402
Phosphate-buffered saline (PBS)	Gibco	Cat#: 15326239
Bacterial and virus strains
Chemically competent DH5α Escherichia coli	Thermo Fisher Scientific	Cat#: 12879416
Biological samples
Human sera, convalescent SARS-Cov-2	This study	N/A
Human sera, post-COVID-19 vaccination	(van Gils et al., 2022)	N/A
Chemicals, peptides, and recombinant proteins
FastDigest SacI	Thermo Fisher Scientific	Cat#: 10324720
FastDigest ApaI	Thermo Fisher Scientific	Cat#: 10450280
Polyethylenimine hydrochloride (PEI) MAX	PolySciences	Cat#: 24765-1
Trypsin-EDTA	Gibco	Cat#: 25-200-056
GlutaMAX	Gibco	Cat#: 35050061
Glycylglycine, 99+%	Acros Organics/Thermo Scientific	Cat#: 120141000
Magnesium sulfate heptahydrate, 99.5%, for analysis, Thermo Scientific™	Acros Organics/ Thermo Scientific	Cat#: AC21311500
EGTA (ethylene glycol bis(2-aminoethyl ether)-N,N,N’,N’-tetraacetic acid) ≥97%, Ultra Pure Grade	VWR	Cat#: 0732-100G
Triton™ X-100 (Electrophoresis), Fisher BioReagents™	Fisher BioReagents	Cat#: BP151-500
Poly-L-Lysine Hydrobromide	Sigma-Aldrich	Cat#: P1399
Critical commercial assays
Gibson Assembly	New England BioLabs	N/A
QuikChange Site-Directed Mutagenesis Kit	Agilent Technologies	Cat#: 200523
Experimental models: Cell lines
HEK293T cells	American Type Culture Collection	CRL-11268
HEK-293T-hACE2	(Schmidt et al., 2020)	RRID:CVCL_A7UK
Oligonucleotides
SARS-CoV-2 D614G spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Alpha spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Beta spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Gamma spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Delta spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Omicron BA.1 spike gene fragment	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
SARS-CoV-2 Omicron BA.2 spike gene fragments	Integrated DNA Technologies	GenBank:MT449663.1 Mutations in this paper
Recombinant DNA
pCR3 SARS-CoV-2–SΔ19 expression plasmid	GenBank	ID: MT449663.1
pHIV-1NL43 ΔEnv-NanoLuc reporter virus plasmid	(Schmidt et al., 2020)	N/A
Software and algorithms
ACMACS antigenic cartography software	https://acmacs-web.antigenic-cartography.org/	N/A
GraphPad Prism 8.3.0	GraphPad	RRID:SCR_002798; http://www.graphpad.com/
Microsoft Excel	Microsoft	RRID:SCR_016137; https://www.microsoft.com/en-gb/
Other
Nano-Glo Luciferase Assay System	Promega	Cat#: N1130
GloMax system	Turner BioSystems	Cat#: 9101-002