Table 3.

Promiscuous CD4+ T-cell epitopes from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) unannotated open reading frame (uORF) proteins are listed along with the number of human leukocyte antigen (HLA) II alleles.

uORF proteins	Positions	Epitope	No. of alleles	CD4+ immunogenicity score	Vaxijen antigenicity score	Population coverage of the alleles	HR/MR mutation	Percentage frequency (%)
3a.iORF1 (ORF3c)	2–16	LLLQILFALLQRYRY	2	35.9554	0.6920	14.77%
	26–40	LLALHFLLFFRALPK	3	38.66696	0.4136	–	R36I	20.18
	4–18	LQILFALLQRYRYKP	2	39.97024	1.1376	14.77%	K17E	1.25
	3–17	LLQILFALLQRYRYK	2	40.33808	0.7138	14.77%	K17E	1.25
M.ext	101–115	VGLMWLSYFIASFRL	2	34.087	0.6658	–
	55–69	RNRFLYIIKLIFLWL	2	39.4372	0.5114	10.54%
	187–201	RTLSYYKLGASQRVA	2	39.12528	0.5644	17.55%
7a.iORF 1	96–110	SPIFLIVAAIVFITL	2	40.0232	0.7118	28.63%
ORF9b & N.iORF2	42–56	YPIILRLGSPLSLNM	2	38.29864	0.6786	28.79%
	43–57	PIILRLGSPLSLNMA	2	38.73068	0.7535	28.79%
	40–54	KVYPIILRLGSPLSL	3	39.42084	0.623	37.64%
	41–55	VYPIILRLGSPLSLN	2	39.58644	0.5837	28.79%
S.iORF 2	24–38	YHLMMVFILLPLRSL	3	40.22584	0.8466
S.iORF1	4–18	GSMLYMSLGPMVLRG	2	38.62404	1.014	17.55%	Y8-, M9-	42.85, 42.97
	3–17	LGSMLYMSLGPMVLR	2	38.86964	1.0898	17.55%	Y8-, M9-	42.85, 42.97
	2–16	LLGSMLYMSLGPMVL	2	39.86928	0.8619	17.55%	Y8-, M9-	42.85, 42.97
	5–19	SMLYMSLGPMVLRGL	2	40.08156	1.0383	17.55%	Y8-, M9-	42.85, 42.97

Note that the residue numbers of an epitope (column 2) located in a particular protein (column 1) and its amino acid sequence (column 3) are given along with its immunogenicity (column 5) and antigenicity (column 6) scores. Note that the number of HLA II alleles to which the epitope bind with (column 4) is also given along with the population coverage of the alleles (column 7). Column 8 represents the HR/MR mutation(s) present in the epitope, if any. The percentage frequencies of the HR/MR mutation(s) are given in column 9. For the uORF HR/MR mutations, refer to Figure 4.