Table 3.

Prediction of B cell and T cell epitopes of 28 epitopes in SARS‐CoV‐2 spike protein

Position in spike protein	Amino acid sequence in spike protein	Average SOA score	B cell epitope prediction		T cell epitope prediction
			ABCpred	IEDB	HLA class I molecule	HLA class II molecule
1025‐1041	AATKMSECVLGQSKRVD	12.33	2‐17	7‐14	N/A	HLA‐DRB1 0101
899‐906	AMQMAYRF	4.06	N/A	0	HLA‐A2402	N/A
749‐771	CSNLLLQYGSFCTQLNRALTGIA	22.79	2‐17	17	HLA‐A0301  HLA‐A2402 HLA‐B0801  HLA‐B1501 HLA‐B2705  HLA‐B3901	HLA‐DRB1 0101  HLA‐DRB1 0301 HLA‐DRB1 0401  HLA‐DRB1 0701 HLA‐DRB1 1501
525‐566	CGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFG	25.59	1‐37	5‐39	HLA‐A0101  HLA‐A0301 HLA‐A1101  HLA‐A2601 HLA‐B0702  HLA‐B0801 HLA‐B1501  HLA‐B3901 HLA‐B3902  HLA‐B5101	HLA‐DRB1 0101  HLA‐DRB1 0301 HLA‐DRB1 0401  HLA‐DRB1 0404 HLA‐DRB1 0701  HLA‐DRB1 1501
525‐574	CGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTD	24.71	2‐21, 24‐43	7‐46	HLA‐A0101  HLA‐A0301 HLA‐A1101  HLA‐A2601 HLA‐B0702  HLA‐B0801 HLA‐B1501  HLA‐B3901 HLA‐B3902  HLA‐B5101	HLA‐DRB1 0101  HLA‐DRB1 0301 HLA‐DRB1 0401  HLA‐DRB1 0404 HLA‐DRB1 0701  HLA‐DRB1 1101 HLA‐DRB1 1501
291‐325	CALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTES	32.24	2‐28	18‐32	HLA‐A0301  HLA‐A1101 HLA‐A2402  HLA‐A2601 HLA‐B5801	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0701  HLA‐DRB1 1101 HLA‐DRB1 1501
15‐44	CVNLTTRTQLPPAYTNSFTRGVYYPDKVFR	31.38	5‐24	5‐26	HLA‐A0101  HLA‐A0201 HLA‐A0301  HLA‐A2601 HLA‐B0702  HLA‐B1501 HLA‐B1516  HLA‐B2705	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0701
379‐395	CYGVSPTKLNDLCFTNV	15.48	1‐16	6‐13	HLA‐A2402	HLA‐DRB1 0301  HLA‐DRB1 0701
307‐323	TVEKGIYQTSNFRVQPT	36.14	1‐16	6‐14	HLA‐A0301  HLA‐A2402 HLA‐B5801	HLA‐DRB1 0701  HLA‐DRB1 1101 HLA‐DRB1 1501
410‐426	IAPGQTGKIADYNYKLP	8.61	2‐17	6‐13	HLA‐A0201  HLA‐B0702 HLA‐B1501  HLA‐B5101	N/A
195‐226	KNIDGYFKIYSKHTPINLVRDLPQGFSALEPL	30.24	3‐22	8‐28	HLA‐A0101  HLA‐A0201 HLA‐A2601  HLA‐B0702 HLA‐B0801  HLA‐B1501 HLA‐B3501  HLA‐B3901 HLA‐B5802	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0404  HLA‐DRB1 0701 HLA‐DRB1 1101  HLA‐DRB1 1501 HLA‐DQA1 0301  HLA‐DQB1 0302
690‐706	QSIIAYTMSLGAENSVA	30.17	1‐16	6‐13	HLA‐A0201  HLA‐A2601 HLA‐B0702  HLA‐B0801 HLA‐B1501  HLA‐B1516 HLA‐B3901  HLA‐B5801	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0402  HLA‐DRB1 0701 HLA‐DRB1 1101  HLA‐DRB1 1501
533‐549	LVKNKCVNFNFNGLTGT	19.67	4‐17	8‐13	HLA‐B0801  HLA‐B1501	HLA‐DRB1 0404  HLA‐DRB1 1501
683‐699	RARSVASQSIIAYTMSL	N/A	2‐15	6‐13	HLA‐A0101  HLA‐A0201 HLA‐A2601  HLA‐B0702 HLA‐B0801  HLA‐B1501 HLA‐B1516  HLA‐B2705 HLA‐B3901  HLA‐B4001 HLA‐B5801  HLA‐B5802	HLA‐DRB1 0101  HLA‐DRB1 0301
754‐770	LQYGSFCTQLNRALTGI	25.03	2‐15	0	HLA‐A0201  HLA‐A0301 HLA‐A1101  HLA‐B1501 HLA‐A2402  HLA‐B2705 HLA‐B3901	HLA‐DRB1 0101  HLA‐DRB1 0301 HLA‐DRB1 0401  HLA‐DRB1 0701
902‐918	MAYRFNGIGVTQNVLYE	12.31	2‐15	6‐13	HLA‐B2705	HLA‐DRB1 0401  HLA‐DRB1 0402 HLA‐DRB1 0404  HLA‐DRB1 1501
897‐913	PFAMQMAYRFNGIGVTQ	12.19	2‐17	10, 12‐13	HLA‐A2402  HLA‐A2601 HLA‐B0801  HLA‐B1501 HLA‐B2705  HLA‐B3901 HLA‐B5801	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0402  HLA‐DRB1 1501
1213‐1229	PWYIWLGFIAGLIAIVM	N/A	1‐16	0	HLA‐A0201  HLA‐A2402 HLA‐A2601  HLA‐B3901	HLA‐DRB1 0101  HLA‐DRB1 0301 HLA‐DRB1 0401  HLA‐DRB1 0402 HLA‐DRB1 0701  HLA‐DRB1 1101 HLA‐DRB1 1501
1019‐1035	RASANLAATKMSECVLG	14.31	2‐17	8‐13	HLA‐A0301  HLA‐A1101 HLA‐B5801	HLA‐DRB1 0101
530‐544	STNLVKNKCVNFNFN	28.43	3‐14	6‐11	HLA‐B0801  HLA‐B1501	HLA‐DRB1 0301
371‐387	SASFSTFKCYGVSPTKL	24.57	3‐16	8‐13	HLA‐A0101  HLA‐A0301 HLA‐A2402  HLA‐B1501 HLA‐B3901  HLA‐B5801	HLA‐DRB1 0401  HLA‐DRB1 1501
747‐763	TECSNLLLQYGSFCTQL	26.54	1‐16	7‐13	HLA‐A0101  HLA‐A2402 HLA‐B0801  HLA‐B1501 HLA‐B3901	HLA‐DRB1 0101  HLA‐DRB1 1501
1129‐1145	VIGIVNNTVYDPLQPEL	37.57	1‐16	5‐13	HLA‐A0201  HLA‐A2402	HLA‐DRB1 0701  HLA‐DRB1 0801
891‐906	GAALQIPFAMQMAYRF	9.67	1‐14	0	HLA‐A2402  HLA‐A2601 HLA‐B0801  HLA‐B1501 HLA‐B3501  HLA‐B3901 HLA‐B4001  HLA‐B5301 HLA‐B5801	HLA‐DRB1 0101  HLA‐DRB1 0401 HLA‐DRB1 0404  HLA‐DRB1 0701 HLA‐DRB1 1501
902‐917	MAYRFNGIGVTQNVLY	11.38	2‐15	5‐12	HLA‐B2705	HLA‐DRB1 0401  HLA‐DRB1 0402 HLA‐DRB1 0404  HLA‐DRB1 1501
1101‐1115	HWFVTQRNFYEPQII	23.55	2‐13	5‐11	HLA‐A2402  HLA‐A2601 HLA‐B2705	HLA‐DRB1 0801
194‐210	FKNIDGYFKIYSKHTPI	22.72	1‐16	9‐13	HLA‐A0101  HLA‐A0201 HLA‐B0702  HLA‐B0801 HLA‐B3901	HLA‐DRB1 1501  HLA‐DQA1 0301 HLA‐DQB1 0302
722‐739	VTTEILPVSMTKTSVDCT	13.03	1‐16	9‐14	HLA‐A0101  HLA‐A0301 HLA‐B1516  HLA‐B3901	HLA‐DRB1 0101  HLA‐DRB1 0701

Note: In the table, the underlined epitopes overlaped with CR3022 epitope published in Science by Yuan et al. ²⁸ The bolded epitopes were consistent with the corresponding epitope sequences in IEDB database. The prediction results of T‐cell epitope and MHC binding combined the results of three analysis tools NetMHC 4.0 Sever, Rankpep and SYFPEITHI. N/A meant undetectable. HLA, human lymphocyte antigen; SOA, solvent accessibility.