Table 1.

Immunogenic SARS-CoV-2 peptides (n = 29) identified by multimer staining in samples from convalescents and pre-pandemic controls sorted from highest to lowest immunoprevalence in convalescents expressing the relevant HLA allele

Peptide	Sequence	HLA allele	Protein	BA_rank (%)	Immunoprevalence (95% CI)		MS	Functional validation	Homology HCoV (%)				Not in the IEDB
					convalescents	pre-pandemic			OC43	NL63	HKU1	229E
N105–113	SPRWYFYYL	B∗07:02	nucleocapsid	0.02	100 (89–100)	57 (18–90)		x	89	56	89	67
O3a207–215	FTSDYYQLY	A∗01:01	ORF3a	0.01	100 (83–100)	0	x	x	0	22	0	0
O3a206–215	YFTSDYYQLY	A∗01:01	ORF3a	0.02	100 (83–100)	0		x	0	0	0	0
S269–277	YLQPRTFLL	A∗02:01	spike	0.02	98 (90–100)	11 (0–48)	x	x	44	44	44	33
O3a139–147	LLYDANYFL	A∗02:01	ORF3a	0.01	91 (79–97)	0		x	0	0	0	0
N366–374	KTFPPTEPK	A∗03:01	nucleocapsid	0.05	90 (73–98)	0	x	x	33	44	44	0
O3a203–212	LHSYFTSDYY	A∗01:01	ORF3a	0.10	86 (57–98)	0			0	30	0	0	x
S378–387	KCYGVSPTKL	A∗03:01	spike	7.90	83 (64–94)	11 (0–48)	x	x	40	30	0	30	x
N257–265	KPRQKRTAT	B∗07:02	nucleocapsid	0.05	70 (46–88)	29 (4–71)			67	67	78	56
O3a72–80	ALSKGVHFV	A∗02:01	ORF3a	0.11	53 (39–67)	0	x	x	0	44	0	0
S89–97	GVYFASTEK	A∗03:01	spike	0.05	45 (26–64)	0		x	33	44	33	33
S865–874	LTDEMIAQYT	A∗01:01	spike	0.12	45 (23–68)	0		x	40	30	40	30	x
N77–87	NSSPDDQIGYY	A∗01:01	nucleocapsid	0.07	36 (13–65)	0	x	x	0	45	27	27
N222–230	LLLDRLNQL	A∗02:01	nucleocapsid	0.14	33 (17–53)	0	x	x	0	0	33	33
O3a35–43	IPIQASLPF	B∗07:02	ORF3a	0.09	30 (12–54)	0			0	0	0	0
S1192–1200	NLNESLIDL	A∗02:01	spike	1.01	30 (15–49)	44 (14–79)	x		56	33	56	56
S864–873	LLTDEMIAQY	A∗01:01	spike	0.01	29 (8–58)	0			40	0	30	30
N66–74	FPRGQGVPI	B∗07:02	nucleocapsid	0.01	25 (9–49)	0		x	67	44	89	44
O3a64–72	TLKKRWQLA	B∗08:01	ORF3a	0.10	21 (5–51)	0			0	33	0	0	x
N104–112	LSPRWYFYY	A∗01:01	nucleocapsid	0.08	21 (5–51)	11 (0–48)			89	89	89	67	x
S109–117	TLDSKTQSL	A∗02:01	spike	1.55	20 (8–39)	11 (0–48)			44	56	44	44
N366–375	KTFPPTEPKK	A∗03:01	nucleocapsid	0.06	17 (4–41)	11 (0–48)			0	0	40	0
N222–230	LLLDRLNQL	B∗08:01	nucleocapsid	0.19	14 (2–43)	29 (4–71)			0	0	33	33	x
S1000–1008	RLQSLQTYV	A∗02:01	spike	0.16	13 (4–31)	0	x		56	44	56	44
S787–795	QIYKTPPIK	A∗03:01	spike	0.14	11 (1–35)	11 (0–48)	x		22	22	22	44
S367–378	VLYNSASFSTFK	A∗03:01	spike	0.01	11 (1–35)	0	x		0	25	0	33	x
O3a204–212	HSYFTSDYY	A∗01:01	ORF3a	0.06	7 (0–34)	0	x		0	0	0	0	x
M65–73	FVLAAVYRI	A∗02:01	membrane	0.11	3 (0–17)	0			22	0	0	22
M50–59	LIFLWLLWPV	A∗02:01	membrane	0.39	3 (0–17)	0			60	50	60	60	x

CI, confidence interval; BA, binding affinity. Functional validation, T cell lines functionally tested; Homology, % sequence identity with human common cold coronaviruses (HCoV); Not in the IEDB, not previously reported as immunogenic in the IEDB.