COVID-19 coronavirus vaccine T cell epitope prediction analysis based on distributions of HLA class I loci (HLA-A, -B, -C) across global populations

Figures & data

Figure 1. The flow chart of epitope prediction analysis and results

Table 1. List of 70 HLA alleles (18 HLA-A alleles, 32 HLA-B alleles, 20 HLA-C alleles) selected occurring in at least 1% of the human population

HLA Allele Loci	Alleles
HLA-A	A*02:01, A*01:01, A*02:06, A*03:01, A*11:01, A*23:01, A*24:02, A*25:01, A*26:01, A*29:02, A*30:01, A*30:02, A*31:01, A*32:01, A*33:03, A*68:01, A*74:01, A*68:02
HLA-B	B*07:02, B*08:01, B*13:01, B*13:02, B*14:02, B*15:01, B*15:02, B*15:25, B*18:01, B*27:02, B*27:05, B*35:01, B*35:03, B*37:01, B*38:01, B*39:01, B*40:01, B*40:02, B*44:02, B*44:03, B*46:01, B*48:01, B*49:01, B*50:01, B*51:01, B*52:01, B*53:01, B*55:01, B*56:01, B*57:01, B*58:01, B*58:02
HLA-C	C*01:02, C*02:02, C*02:09, C*03:02, C*03:03, C*03:04, C*04:01, C*05:01, C*06:02, C*07:01, C*07:02, C*07:04, C*08:01, C*08:02, C*12:02, C*12:03, C*14:02, C*15:02, C*16:01, C*17:01

Table 2. The epitopes number, cluster numbers, and population coverage results of the predicted SARS-CoV-2 N and S proteins

Protein	Epitopes Number	Total Score	Population Coverage			Clustering
			coverage^a	Average hit^b	PC90^c
N protein	130	0.30	0.9910	8.18	2.44	21
	110	0.40	0.9903	7.25	2.28	17
	103	0.45	0.9903	6.57	2.13	17
	99	0.47	0.9665	5.99	1.64	17
	90	0.50	0.9591	5.57	1.51	16
	82	0.55	0.9458	4.97	1.32	15
	71	0.60	0.9228	4.39	1.14	15
S protein	313	0.70	0.9901	19.77	4.78	57
	247	0.80	0.9864	16.12	4.33	49
	179	0.90	0.9810	12.09	3.31	45
	158	0.95	0.9788	10.65	3.23	40
	133	1.00	0.9632	8.65	1.60	35
	113	1.05	0.9614	7.35	1.56	33
	106	1.07	0.9614	7.08	1.56	34
	95	1.10	0.9319	6.17	1.28	33
	80	1.15	0.9242	5.25	1.17	30

^aprojected population coverage

^baverage number of epitope hits/HLA combinations recognized by the population

^cminimum number of epitope hits/HLA combinations recognized by 90% of the population

Table 3. The epitopes sequences, amino acid position and its presented HLA alleles of SARS-CoV-2 N protein by cluster analysis

Cluster Number	Epitope Number	Alignment	Epitope	Amino-acid Position	HLA Alleles
1.1	Consensus	DGKMKDLSPRWYFYYL	-	98–113
	1	DGKMKDLSPRWYFY–	DGKMKDLSPRWYFY	98–111	A*30:02
	2	-GKMKDLSPRWYFY–	GKMKDLSPRWYFY	99–111	A*30:02, A*29:02
	3	–KMKDLSPRWYFYY-	KMKDLSPRWYFYY	100–112	A*30:02, A*29:02
	4	–KMKDLSPRWYFY–	KMKDLSPRWYFY	100–111	A*30:02, A*29:02, A*30:01, A*31:01
	5	–KMKDLSPRWY – -	KMKDLSPRWY	100–109	A*30:02, B*15:25, B*15:01
	6	– MKDLSPRWYFY–	MKDLSPRWYFY	101–111	A*29:02, A*30:02
	7	– -KDLSPRWYFY–	KDLSPRWYFY	102–111	A*30:02, A*03:01, A*29:02
	8	– –DLSPRWYFYY-	DLSPRWYFYY	103–112	A*29:02
	9	– –DLSPRWYFY–	DLSPRWYFY	103–111	A*29:02
	10	– – LSPRWYFYY-	LSPRWYFYY	104–112	A*29:02, A*30:02
	11	– – -SPRWYFYYL	SPRWYFYYL	105–113	B*07:02, B*08:01
2.1	Consensus	IAQFAPSASAFF	-	304–315
	1	IAQFAPSASAF-	IAQFAPSASAF	304–314	B*15:25
	2	-AQFAPSASAFF	AQFAPSASAFF	305–315	B*15:01, B*15:25
	3	-AQFAPSASAF-	AQFAPSASAF	305–314	B*15:25, B*15:01, B*15:02
	4	–QFAPSASAFF	QFAPSASAFF	306–315	A*23:01
	5	–QFAPSASAF-	QFAPSASAF	306–314	C*14:02
	6	– FAPSASAFF	FAPSASAFF	307–315	C*12:03, B*35:01, C*03:03, C*03:04, C*03:02, C*14:02, C*16:01
3.1	Consensus	MSRIGMEVTPSGTWLTY	-	317–333
	1	MSRIGMEVTPSGTW –	MSRIGMEVTPSGTW	317–330	B*58:01
	2	– –MEVTPSGTWLTY	MEVTPSGTWLTY	322–333	B*35:01, B*18:01, B*44:03
	3	– –MEVTPSGTW –	MEVTPSGTW	322–330	B*44:02
	4	– – -VTPSGTWLTY	VTPSGTWLTY	324–333	A*29:02, B*35:01, A*30:02
	5	– – –TPSGTWLTY	TPSGTWLTY	325–333	B*35:01, B*53:01
4.1	Consensus	NTNSSPDDQIGYY	-	75–87
	1	NTNSSPDDQIGYY	NTNSSPDDQIGYY	75–87	A*01:01
	2	–NSSPDDQIGYY	NSSPDDQIGYY	77–87	A*01:01
	3	– SSPDDQIGYY	SSPDDQIGYY	78–87	A*01:01
	4	– -SPDDQIGYY	SPDDQIGYY	79–87	B*35:01
5.1	Consensus	FYYLGTGPEAGLPY	-	110–123
	1	FYYLGTGPEAGLPY	FYYLGTGPEAGLPY	110–123	A*29:02, C*14:02
	2	-YYLGTGPEAGLPY	YYLGTGPEAGLPY	111–123	A*29:02
6.1	Consensus	LPQGTTLPKGFY	-	161–172
	1	LPQGTTLPKGFY	LPQGTTLPKGFY	161–172	B*35:01
	2	– GTTLPKGFY	GTTLPKGFY	164–172	A*30:02
7.1	Consensus	ILLNKHIDAY	-	351–360
	1	ILLNKHIDAY	ILLNKHIDAY	351–360	B*15:25, B*15:01
	2	-LLNKHIDAY	LLNKHIDAY	352–360	B*15:25, B*15:01, B*15:02
8.1	Consensus	KFPRGQGVPI	-	65–74
	1	KFPRGQGVPI	KFPRGQGVPI	65–74	B*07:02
	2	-FPRGQGVPI	FPRGQGVPI	66–74	B*07:02
9.1	Singleton	NTASWFTAL	NTASWFTAL	48–56	A*68:02
10.1	Singleton	RQKRTATKAY	RQKRTATKAY	259–268	B*15:01, B*15:25, A*30:02
11.1	Singleton	KAYNVTQAF	KAYNVTQAF	266–274	C*03:02, B*15:25, C*12:03, A*32:01, C*16:01, C*03:03, C*03:04, B*15:01, C*14:02, B*58:01, C*12:02, B*15:02, B*35:01, C*02:09, C*02:02
12.1	Singleton	LPAADLDDF	LPAADLDDF	395–403	B*35:01
13.1	Singleton	LPNNTASWF	LPNNTASWF	45–53	B*35:01, B*53:01
14.1	Singleton	LLLDRLNQL	LLLDRLNQL	222–230	A*02:01, A*02:06
15.1	Singleton	IGYYRRATR	IGYYRRATR	84–92	A*31:01
16.1	Singleton	NQRNAPRITF	NQRNAPRITF	8–17	B*15:01

Table 4. The epitopes sequences, amino acid position and its presented HLA alleles of SARS-CoV-2 S protein by cluster analysis

Cluster Number	Epitope Number	Alignment	Epitope	Amino-acid Position	HLA Alleles
1.1	Consensus	YSVLYNSASFSTFKCY	-	365–380
	1	YSVLYNSASF – –	YSVLYNSASF	365–374	B*15:01
	2	-SVLYNSASF – –	SVLYNSASF	366–374	B*15:25
	3	–VLYNSASFSTFKCY	VLYNSASFSTFKCY	367–380	A*03:01
	4	– LYNSASFSTF –	LYNSASFSTF	368–377	A*23:01, A*24:02
	5	– – -ASFSTFKCY	ASFSTFKCY	372–380	B*15:25, A*30:02
2.1	Consensus	AYYVGYLQPRTFLLKY	-	264–279
	1	AYYVGYLQPRTF – -	AYYVGYLQPRTF	264–275	A*23:01
	2	-YYVGYLQPRTF – -	YYVGYLQPRTF	265–275	A*23:01
	3	– -GYLQPRTFLLKY	GYLQPRTFLLKY	268–279	A*29:02
	4	– –YLQPRTFLLKY	YLQPRTFLLKY	269–279	A*29:02
	5	– –YLQPRTFLL–	YLQPRTFLL	269–277	A*02:01
3.1	Consensus	RISNCVADYSVLY	-	357–369
	1	RISNCVADYSVLY	RISNCVADYSVLY	357–369	A*30:02
	2	RISNCVADY – -	RISNCVADY	357–365	A*30:02
	3	– NCVADYSVLY	NCVADYSVLY	360–369	A*29:02
	4	– -CVADYSVLY	CVADYSVLY	361–369	A*29:02, B*35:01, A*26:01, A*01:01
4.1	Consensus	LQIPFAMQMAYRF	-	894–906
	1	LQIPFAMQMAY–	LQIPFAMQMAY	894–904	B*35:01, B*15:25, B*15:01
	2	-QIPFAMQMAY–	QIPFAMQMAY	895–904	B*35:01, A*29:02
	3	–IPFAMQMAY–	IPFAMQMAY	896–904	B*35:01, B*53:01
	4	– -FAMQMAYRF	FAMQMAYRF	898–906	B*35:01, C*03:02, B*53:01, C*03:04, C*03:03, B*58:01, A*23:01
5.1	Consensus	RVYSSANNCTFEY	-	158–170
	1	RVYSSANNCTFEY	RVYSSANNCTFEY	158–170	A*30:02
	2	-VYSSANNCTF–	VYSSANNCTF	159–168	A*24:02
	3	–YSSANNCTF–	YSSANNCTF	160–168	C*03:02, C*03:04, C*03:03, B*35:01, C*16:01, C*12:03
	4	– -SANNCTFEY	SANNCTFEY	162–170	B*35:01, A*29:02
6.1	Consensus	AYTMSLGAENSVAY	-	694–707
	1	AYTMSLGAENSVAY	AYTMSLGAENSVAY	694–707	A*29:02
	2	-YTMSLGAENSVAY	YTMSLGAENSVAY	695–707	A*29:02, B*15:25
	3	– -SLGAENSVAY	SLGAENSVAY	698–707	B*15:25
	4	– –LGAENSVAY	LGAENSVAY	699–707	B*35:01
7.1	Consensus	SWMESEFRVY	-	151–160
	1	SWMESEFRVY	SWMESEFRVY	151–160	A*29:02
	2	-WMESEFRVY	WMESEFRVY	152–160	B*15:25, B*15:02
	3	–MESEFRVY	MESEFRVY	153–160	B*18:01
8.1	Consensus	YTNSFTRGVYY	-	28–38
	1	YTNSFTRGVYY	YTNSFTRGVYY	28–38	A*01:01, A*29:02
	2	YTNSFTRGVY-	YTNSFTRGVY	28–37	A*30:02, A*01:01
	3	–NSFTRGVYY	NSFTRGVYY	29–38	C*12:03, A*29:02
9.1	Consensus	HWFVTQRNFY	-	1101–1110
	1	HWFVTQRNFY	HWFVTQRNFY	1101–1110	A*29:02
	2	-WFVTQRNFY	WFVTQRNFY	1102–1110	A*29:02
10.1	Consensus	FQFCNDPFLGVY	-	133–144
	1	FQFCNDPFLGVY	FQFCNDPFLGVY	133–144	B*15:25, B*15:01
	2	FQFCNDPFL –	FQFCNDPFL	133–141	A*02:06
11.1	Consensus	SVASQSIIAY	-	686–695
	1	SVASQSIIAY	SVASQSIIAY	686–695	B*15:25
	2	-VASQSIIAY	VASQSIIAY	687–695	B*35:01, B*15:25, C*03:02
12.1	Consensus	FLPFFSNVTW	-	55–64
	1	FLPFFSNVTW	FLPFFSNVTW	55–64	B*53:01
	2	-LPFFSNVTW	LPFFSNVTW	56–64	B*53:01
13.1	Consensus	KRSFIEDLLF	-	814–823
	1	KRSFIEDLLF	KRSFIEDLLF	814–823	B*58:01
	2	-RSFIEDLLF	RSFIEDLLF	815–823	B*58:01, B*57:01
14.1	Consensus	LLTDEMIAQY	-	864–873
	1	LLTDEMIAQY	LLTDEMIAQY	864–873	A*01:01
	2	-LTDEMIAQY	LTDEMIAQY	865–873	A*01:01
15.1	Consensus	RVYSTGSNVF	-	634–643
	1	RVYSTGSNVF	RVYSTGSNVF	634–643	B*15:25, B*15:01, A*32:01
	2	-VYSTGSNVF	VYSTGSNVF	635–643	C*14:02
16.1	Singleton	WTAGAAAYY	WTAGAAAYY	258–266	A*29:02, A*26:01, A*68:01
17.1	Singleton	KWPWYIWLGF	KWPWYIWLGF	1211–1220	A*23:01, A*24:02
18.1	Singleton	KSNIIRGWIF	KSNIIRGWIF	97–106	B*58:01
19.1	Singleton	CYFPLQSYGF	CYFPLQSYGF	488–497	A*23:01, A*24:02
20.1	Singleton	FEYVSQPFL	FEYVSQPFL	168–176	B*40:01
21.1	Singleton	FVFKNIDGY	FVFKNIDGY	192–200	B*35:01, A*29:02
22.1	Singleton	LMSFPQSAPHGVVF	LMSFPQSAPHGVVF	1057–1070	B*15:01, B*15:25
23.1	Singleton	NATRFASVY	NATRFASVY	151–159	B*35:01
24.1	Singleton	KSFTVEKGIY	KSFTVEKGIY	312–321	A*30:02
25.1	Singleton	LPFNDGVYF	LPFNDGVYF	84–92	B*35:01, B*53:01
26.1	Singleton	TLLALHRSY	TLLALHRSY	248–256	B*15:25
27.1	Singleton	NDLCFTNVY	NDLCFTNVY	396–404	B*18:01
28.1	Singleton	YEQYIKWPWY	YEQYIKWPWY	1214–1223	B*18:01
29.1	Singleton	KRFDNPVLPF	KRFDNPVLPF	77–86	B*27:05
30.1	Singleton	FPNITNLCPF	FPNITNLCPF	337–346	B*35:01
31.1	Singleton	NVYADSFVIR	NVYADSFVIR	402–411	A*68:01
32.1	Singleton	QLTPTWRVY	QLTPTWRVY	636–644	B*15:25, B*15:02
33.1	Singleton	KVGGNYNYLY	KVGGNYNYLY	452–461	A*30:02
34.1	Singleton	WTFGAGAAL	WTFGAGAAL	894–902	C*03:04, C*03:03

Table 5. The results of comparing N and S protein of SARS-CoV-2 with Bat coronavirus and other human coronaviruses (SARS, MERS, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63)

Serial number	complete genome^a	Genus	Subgenus	Description	Max Score	Total Score	Query Cover^b	E value^c	Per. Ident^d	Accession
1	NC_045512.2	Betacoronavirus	Sarbecovirus	nucleocapsid phosphoprotein	854	854	100%	0	100.00%	YP_009724397.2
				surface glycoprotein	2637	2637	100%	0	100.00%	YP_009724390.1
2	MT007544.1	Betacoronavirus	Sarbecovirus	nucleocapsid phosphoprotein	854	854	100%	0	100.00%	QHR84456.1
				surface glycoprotein	2634	2634	100%	0	99.92%	QHR84449.1
3	MG772934.1	Betacoronavirus	Sarbecovirus	nucleocapsid protein	715	715	100%	0	94.27%	AVP78049.1
				spike protein	2105	2105	99%	0	80.32%	AVP78042.1
4	KT444582.1	Betacoronavirus	Sarbecovirus	nucleocapsid protein	669	669	100%	0	90.28%	ALK02467.1
				spike protein	2065	2065	100%	0	77.07%	ALK02457.1
5	KY417144.1	Betacoronavirus	Sarbecovirus	nucleocapsid protein	666	666	100%	0	90.05%	ATO98142.1
				spike protein	2049	2049	99%	0	77.23%	ATO98132.1
6	FJ882944.1	Betacoronavirus	Sarbecovirus	nucleocapsid protein	672	672	100%	0	90.52%	ACZ72030.1
				spike glycoprotein precursor	2040	2040	100%	0	76.12%	ACZ72020.1
7	NC_004718.3	Betacoronavirus	Sarbecovirus	nucleocapsid protein	672	672	100%	0	90.52%	YP_009825061.1
				spike glycoprotein precursor	2038	2038	100%	0	75.96%	YP_009825051.1
8	MG987420.1	Betacoronavirus	Merbecovirus	N protein	288	288	88%	6E-90	50.26%	AWH65950.1
				S protein	561	636	85%	0	35.56%	AWH65943.1
9	MG021451.1	Betacoronavirus	Merbecovirus	N protein	284	284	82%	3E-88	50.97%	AVV62533.1
				S protein	556	618	83%	1E-179	34.70%	AVV62526.1
10	NC_006213.1	Betacoronavirus	Embecovirus	nucleocapsid protein	176	207	74%	6.00E-55	38.35%	YP_009555245.1
				spike surface glycoprotein	467	602	74%	2.00E-146	37.63%	YP_009555241.1
11	NC_006577.2	Betacoronavirus	Embecovirus	nucleocapsid phosphoprotein	197	212	82%	9.00E-63	36.74%	YP_173242.1
				spike glycoprotein	452	576	71%	3.00E-141	35.43%	YP_173238.1
12	KY983587.1	Alphacoronavirus	Duvinacovirus	nucleocapsid protein	89.4	89.4	65%	6.00E-24	29.43%	ARU07605.1
				spike protein	366	481	67%	2.00E-111	31.32%	ARU07601.1
13	NC_005831.2	Alphacoronavirus	Setracovirus	nucleocapsid protein	61.2	61.2	13%	9.00E-15	48.28%	YP_003771.1
				Spike protein	349	404	65%	3.00E-104	30.78%	YP_003767.1

^aNC_045512.2 is Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1;

MT007544.1 is Severe acute respiratory syndrome coronavirus 2 isolate Australia/VIC01/2020;

MG772934.1 is Bat SARS-like coronavirus isolate bat-SL-CoVZXC21;

KY417144.1 is Bat SARS-like coronavirus isolate Rs4084;

KT444582.1 is SARS-like coronavirus WIV16;

FJ882944.1 is SARS coronavirus ExoN1 isolate P3pp23;

NC_004718.3 SARS coronavirus Tor2;

MG987420.1 is Middle East respiratory syndrome-related coronavirus isolate NL13892;

MG021451.1 is Middle East respiratory syndrome-related coronavirus isolate NL13845;

NC_006213.1 Human coronavirus OC43 strain ATCC VR-759;

NC_006577.2 Human coronavirus HKU1;

KY983587.1 Human coronavirus 229E strain HCoV_229E/Seattle/USA/SC3112/2015;

NC_005831.2 Human Coronavirus NL63;

^bQuery Coverage: coverage of the compared sequences

^cexpect value: the possibility of random matching. When the value of E is close to zero or zero, it is essentially a perfect match.

^dpercentage identity: the percentage of base number in the total sequence of the compared sequences

Table 6. The epitope conservancy analysis results for N protein among the 13 coronaviruses

				Identity percentage (%)^d
Name^a	Epitope sequence	Length^b	Percent of protein sequence matches^c	YP_009724397.2	QHR84456.1	AVP78049.1	ALK02467.1	ATO98142.1	ACZ72030.1	YP_009825061.1	AWH65950.1	AVV62533.1	YP_009555245.1	YP_173242.1	ARU07605.1	YP_003771.1
NP 1	DGKMKDLSPRWYFYYL98-113^e	16	15.38% (2/13)	100.00	100.00	93.75	93.75	93.75	93.75	93.75	50.00	50.00	68.75	75.00	62.50	50.00
NP 2	IAQFAPSASAFF304-315	12	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	66.67	66.67	58.33	50.00	33.33	33.33
NP 3	MSRIGMEVTPSGTWLTY317-333	17	46.15% (6/13)	100.00	100.00	100.00	100.00	94.12	100.00	100.00	23.53	23.53	23.53	23.53	29.41	23.53
NP 4	NTNSSPDDQIGYY75-87	13	15.38% (2/13)	100.00	100.00	92.31	92.31	92.31	92.31	92.31	46.15	46.15	30.77	30.77	30.77	38.46
NP 5	FYYLGTGPEAGLPY110-123	14	23.08% (3/13)	100.00	100.00	100.00	92.86	92.86	92.86	92.86	78.57	78.57	71.43	71.43	57.14	64.29
NP 6	LPQGTTLPKGFY161-172	12	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	50.00	50.00	58.33	58.33	33.33	41.67
NP 7	ILLNKHIDAY351-360	10	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	60.00	60.00	40.00	40.00	30.00	30.00
NP 8	KFPRGQGVPI65-74	10	15.38% (2/13)	100.00	100.00	90.00	90.00	90.00	90.00	90.00	70.00	70.00	70.00	80.00	40.00	50.00
NP 9	NTASWFTAL48-56	9	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	66.67	44.44	44.44	33.33	33.33	33.33
NP 10	RQKRTATKAY259-268	10	15.38% (2/13)	100.00	100.00	90.00	90.00	90.00	90.00	90.00	60.00	60.00	50.00	60.00	40.00	40.00
NP 11	KAYNVTQAF266-274	9	15.38% (2/13)	100.00	100.00	88.89	88.89	77.78	88.89	88.89	55.56	55.56	44.44	55.56	55.56	44.44
NP 12	LPAADLDDF395-403	9	15.38% (2/13)	100.00	100.00	88.89	88.89	88.89	88.89	88.89	33.33	33.33	44.44	44.44	44.44	44.44
NP 13	LPNNTASWF45-53	9	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	66.67	44.44	44.44	33.33	44.44	44.44
NP 14	LLLDRLNQL222-230	9	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	55.56	55.56	33.33	33.33	33.33	33.33
NP 15	IGYYRRATR84-92	9	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	55.56	55.56	44.44	44.44	44.44	44.44
NP 16	NQRNAPRITF8-17	10	15.38% (2/13)	100.00	100.00	80.0	90.00	90.00	90.00	90.00	40.00	40.00	30.00	30.00	30.00	40.00

^aepitope name

^bepitope length

^cPercent of protein sequence matches at identity 100%

^dthe identity percentage results of each16 epitopes with 13 N protein sequences

^eAmino-acid position

Table 7. The epitope conservancy analysis results for S protein among the 13 coronaviruses

				Identity percentage (%)^d
Name^a	Epitope sequence	Length^b	Percent of protein sequence matches^c	YP_009724390.1	QHR84449.1	AVP78042.1	ALK02457.1	ATO98132.1	ACZ72020.1	YP_009825051.1	AWH65943.1	AVV62526.1	YP_009555241.1	YP_173238.1	ARU07601.1	YP_003767.1
NP 1	YSVLYNSASFSTFKCY365-380^e	16	15.38% (2/13)	100.00	100.00	81.25	93.75	87.50	87.50	87.50	31.25	31.25	31.25	37.50	31.25	31.25
NP 2	AYYVGYLQPRTFLLKY264-279	16	15.38% (2/13)	100.00	100.00	81.25	75.00	75.00	75.00	75.00	37.50	37.50	37.50	43.75	31.25	37.50
NP 3	RISNCVADYSVLY357-369	13	23.08% (3/13)	100.00	100.00	61.54	100.00	92.31	92.31	92.31	30.77	38.46	38.46	46.15	38.46	38.46
NP 4	LQIPFAMQMAYRF894-906	13	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	46.15	46.15	30.77	38.46	38.46	30.77
NP 5	RVYSSANNCTFEY158-170	13	15.38% (2/13)	100.00	100.00	69.23	53.85	53.85	53.85	53.85	38.46	38.46	30.77	38.46	30.77	38.46
NP 6	AYTMSLGAENSVAY694-707	14	15.38% (2/13)	100.00	100.00	92.86	78.57	78.57	78.57	78.57	42.86	42.86	35.71	28.57	35.71	35.71
NP 7	SWMESEFRVY151-160	10	15.38% (2/13)	100.00	100.00	50.00	40.00	40.00	40.00	40.00	30.00	40.00	40.00	40.00	40.00	30.00
NP 8	YTNSFTRGVYY28-38	11	15.38% (2/13)	100.00	100.00	81.82	54.55	54.55	54.55	54.55	36.36	36.36	36.36	36.36	36.36	36.36
NP 9	HWFVTQRNFY1101-1110	10	23.08% (3/13)	100.00	100.00	100.00	70.00	70.00	70.00	70.00	30.00	30.00	40.00	40.00	30.00	40.00
NP 10	FQFCNDPFLGVY133-144	12	15.38% (2/13)	100.00	100.00	58.33	41.67	41.67	41.67	41.67	33.33	33.33	33.33	33.33	33.33	33.33
NP 11	SVASQSIIAY686-695	10	15.38% (2/13)	100.00	100.00	40.00	50.00	50.00	50.00	50.00	40.00	40.00	40.00	40.00	50.00	50.00
NP 12	FLPFFSNVTW55-64	10	15.38% (2/13)	100.00	100.00	80.00	80.00	80.00	80.00	80.00	40.00	40.00	40.00	40.00	40.00	40.00
NP 13	KRSFIEDLLF814-823	10	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	80.00	90.00	80.00	80.00	70.00	70.00
NP 14	LLTDEMIAQY864-873	10	15.38% (2/13)	100.00	100.00	90.00	80.00	80.00	80.00	80.00	40.00	50.00	40.00	40.00	40.00	40.00
NP 15	RVYSTGSNVF634-643	10	15.38% (2/13)	100.00	100.00	50.00	90.00	90.00	80.00	80.00	40.00	50.00	30.00	40.00	40.00	40.00
NP 16	WTAGAAAYY258-266	9	15.38% (2/13)	100.00	100.00	66.67	55.56	55.56	55.56	55.56	44.44	44.44	44.44	33.33	44.44	33.33
NP 17	KWPWYIWLGF1211-1220	10	30.77% (4/13)	100.00	100.00	90.00	90.00	90.00	90.00	90.00	100.00	100.00	70.00	70.00	60.00	60.00
NP 18	KSNIIRGWIF97-106	10	15.38% (2/13)	100.00	100.00	80.00	70.00	80.00	70.00	70.00	40.00	30.00	40.00	40.00	40.00	40.00
NP 19	CYFPLQSYGF488-497	10	15.38% (2/13)	100.00	100.00	40.00	70.00	70.00	70.00	70.00	40.00	50.00	40.00	40.00	40.00	40.00
NP 20	FEYVSQPFL168-176	9	15.38% (2/13)	100.00	100.00	66.67	55.56	66.67	55.56	55.56	44.44	44.44	44.44	44.44	33.33	44.44
NP 21	FVFKNIDGY192-200	9	15.38% (2/13)	100.00	100.00	66.67	77.78	66.67	77.78	77.78	44.44	44.44	44.44	33.33	44.44	44.44
NP 22	LMSFPQSAPHGVVF1057-1070	14	23.08% (3/13)	100.00	100.00	100.00	92.86	92.86	92.86	92.86	42.86	42.86	42.86	42.86	42.86	42.86
NP 23	NATRFASVY151-159	9	15.38% (2/13)	100.00	100.00	88.89	77.78	77.78	77.78	77.78	55.56	55.56	44.44	44.44	44.44	44.44
NP 24	KSFTVEKGIY312-321	10	15.38% (2/13)	100.00	100.00	70.00	70.00	70.00	70.00	70.00	50.00	50.00	50.00	40.00	50.00	40.00
NP 25	LPFNDGVYF84-92	9	15.38% (2/13)	100.00	100.00	66.67	77.78	66.67	66.67	66.67	44.44	44.44	44.44	55.56	33.33	44.44
NP 26	TLLALHRSY248-256	9	7.69% (1/13)	100.00	88.89	55.56	33.33	33.33	33.33	33.33	44.44	44.44	44.44	55.56	33.33	44.44
NP 27	NDLCFTNVY396-404	9	15.38% (2/13)	100.00	100.00	77.78	88.89	88.89	88.89	88.89	44.44	55.56	44.44	44.44	44.44	55.56
NP 28	YEQYIKWPWY1214-1223	10	46.15% (6/13)	100.00	100.00	90.00	100.00	100.00	100.00	100.00	70.00	70.00	80.00	80.00	70.00	70.00
NP 29	KRFDNPVLPF77-86	10	15.38% (2/13)	100.00	100.00	70.00	80.00	60.00	60.00	60.00	40.00	40.00	30.00	30.00	40.00	40.00
NP 30	FPNITNLCPF337-346	10	46.15% (6/13)	100.00	100.00	90.00	100.00	100.00	100.00	100.00	40.00	40.00	50.00	40.00	40.00	40.00
NP 31	NVYADSFVIR402-411	10	15.38% (2/13)	100.00	100.00	70.00	80.00	80.00	80.00	80.00	40.00	40.00	40.00	40.00	50.00	40.00
NP 32	QLTPTWRVY636-644	9	15.38% (2/13)	100.00	100.00	77.78	88.89	88.89	77.78	77.78	44.44	33.33	44.44	44.44	44.44	44.44
NP 33	KVGGNYNYLY452-461	10	15.38% (2/13)	100.00	100.00	40.00	60.00	70.00	60.00	60.00	50.00	40.00	40.00	40.00	30.00	40.00
NP 34	WTFGAGAAL894-902	9	53.85% (7/13)	100.00	100.00	100.00	100.00	100.00	100.00	100.00	44.44	44.44	44.44	44.44	44.44	44.44

^aepitope name

^bepitope length

^cPercent of protein sequence matches at identity 100%

^dthe identity percentage results of each 34 epitopes with 13 S protein sequences

^eAmino-acid position

Table 8. The epitope sequences and its presented HLA alleles of the 14 combination epitopes

Protein	Epitope sequence	HLA Alleles
N protein	IAQFAPSASAFF304-315^a	A*23:01, B*15:01, B*15:02, B*15:25, B*35:01, C*03:02, C*03:03, C*03:04, C*12:03, C*14:02, C*16:01
	MSRIGMEVTPSGTWLTY317-333	A*29:02, A*30:02, B*18:01, B*35:01, B*44:02, B*44:03, B*53:01, B*58:01
	LPQGTTLPKGFY161-172	A*30:02, B*35:01
	ILLNKHIDAY351-360	B*15:25, B*15:01, B*15:02
	NTASWFTAL48-56	A*68:02
	LPNNTASWF45-53	B*35:01, B*53:01
	LLLDRLNQL222-230	A*02:01, A*02:06
	IGYYRRATR84-92	A*31:01
S protein	LQIPFAMQMAYRF894-906	A*23:01, A*29:02, B*15:01, B*15:25, B*35:01, B*53:01, B*58:01, C*03:02, C*03:03, C*03:04
	KRSFIEDLLF814-823	B*58:01, B*57:01
	YEQYIKWPWY1214-1223	B*18:01
	FPNITNLCPF337-346	B*35:01
	WTFGAGAAL894-902	C*03:04, C*03:03
	KWPWYIWLGF1211-1220	A*23:01, A*24:02

^aAmino-acid position

Table 9. The population coverage results (%) of the 14 combination epitopes

Description	Total Score	Population Coverage
		Coverage^a	Average hit^b	PC90^c
8 epitopes in N protein	0.50	0.8413	1.93	0.63
5 epitopes in S protein	1.07	0.5312	1.02	0.21
8 epitopes in N protein and 5 clusters in S protein	-	0.8494	2.95	0.66
14 epitopes for SARS-CoV-2 (NC_045512.2 and MT007544.1)	-	0.8960	3.22	0.96
13 epitopes for SARS-CoV (FJ882944.1 and NC_004718.3)	-	0.8494	2.95	0.66
13 epitopes for SARS-like coronavirus (KT444582.1)	-	0.8494	2.95	0.66
12 epitopes for Bat SARS-like coronavirus (KY417144.1)	-	0.8191	2.53	0.55
11 epitopes for Bat SARS-like coronavirus (MG772934.1)	-	0.8494	2.79	0.66
1 epitope (NP17 in S protein) for MERS (MG987420.1 and MG021451.1)	-	0.2618	0.27	0.14

^aprojected population coverage

^baverage number of epitope hits/HLA combinations recognized by the population

^cminimum number of epitope hits/HLA combinations recognized by 90% of the population