Table 2.

HLA‐DRB1 binding data generated for frequently recognised spike peptide specificities. For each peptide, in vitro‐generated and in silico‐predicted DRB1 molecule binding and the response frequencies measured in our study are shown. Where available, HLA restrictions from previous studies are referenced. Bold font indicates the most likely HLA restriction.

Peptide		DRB1*01:01	DRB1*03:01	DRB1*04:01	DRB1*04:05	DRB1*07:01	DRB1*08:02	DRB1*09:01	DRB1*11:01	DRB1*12:01	DRB1*13:02	DRB1*15:01	alleles bound	other reported class II restrictions
27 CEFQFCNDPFLGVYY aa131‐145	in vitro binding capacity (IC50)	> 40000	> 40000	6958	4506	27456	> 40000	13478	> 40000	> 40000	> 40000	7645	0	DQB1*05:02, DQB1*05:03 [50]
	in silico prediction (percentile)	46	29	32	50	52	77	25	64	23	48	35
	responding patients	4/6	2/3	4/4	‐	5/8	‐	‐	3/3	0/1	‐	3/7
	HLA restriction references
34 CTFEYVSQPFLMDLE aa166‐180	in vitro binding capacity (IC50)	495	5858	1152	16	15	1465	< 0,2	3382	416	> 40000	7244	5	DRB1*16:01, DQB1*02:01, DQB1*02:02, DQB1*05:02, DQB1*05:03 [50]
	in silico prediction (percentile)	15	64	24	9.3	12	59	7.8	33	40.5	43	30
	responding patients	6/6	3/3	4/4	‐	7/8	‐	‐	3/3	0/1	‐	5/7
	HLA restriction references					[50]
41 FKIYSKHTPINLVRD aa201‐215	in vitro binding capacity (IC50)	64	> 40000	5252	16281	2.7	125	13	229	7183	9039	611	6	DRB1*13:01 [50]
	in silico prediction (percentile)	21	59	24	32	4.2	6.2	8.8	14	39	9.2	28		DRB3 [51]
	responding patients	3/6	0/3	0/4	‐	5/8	‐	‐	0/3	1/1	‐	3/7
	HLA restriction references					[51], [50]
48 TRFQTLLALHRSYLT aa236‐250	in vitro binding capacity (IC50)	38	13801	337	794	3.9	177	11	14	18	29886	5	9	DRB1*14:01, DQB1*05:03 [50]
	in silico prediction (percentile)	0.91	25	1.2	1.5	4.1	12	31	2	1.79	26	1.2		DRB1*04:04, DRB5 [51]
	responding patients	2/6	1/3	1/4	‐	4/8	‐	‐	2/3	1/1	‐	5/7		DRB1*15:02 [53]
	HLA restriction references	[52]		[52]						[50]		[51], [52]
63 GIYQTSNFRVQPTES aa311‐325	in vitro binding capacity (IC50)	2392	> 40000	62	201	12	> 40000	305	1144	2072	10685	21	5
	in silico prediction (percentile)	37	75	42	37	17	53	36	38	34.5	21	19
	responding patients	2/6	1/3	3/4	‐	5/8	‐	‐	1/3	1/1	‐	2/7
	HLA restriction references	[51]		[51]		[51]
69 VFNATRFASVYAWNR aa341‐355	in vitro binding capacity (IC50)	1030	> 40000	853	976	2.7	3712	321	372	500	> 40000	12	7
	in silico prediction (percentile)	19	58	25	13	5.3	19	18	15	31	43	5.4
	responding patients	3/6	1/3	1/4	‐	2/8	‐	‐	1/3	0/1	‐	7/7
	HLA restriction references
70 RFASVYAWNRKRISN aa346‐360	in vitro binding capacity (IC50)	5926	> 40000	7894	6272	540	64	1380	3.9	31627	> 40000	136	4	DRB1*13:01, DRB1*14:01 [50]
	in silico prediction (percentile)	21	29	46	36	20	38	26	1.2	62.5	49	24		DRB5 [51]
	responding patients	5/6	0/3	1/4	‐	3/8	‐	‐	2/3	1/1	‐	7/7
	HLA restriction references		[51]			[50]			[51]
71 YAWNRKRISNCVADY aa351‐365	in vitro binding capacity (IC50)	22040	> 40000	865	3811	> 40000	852	> 40000	37	3673	12685	851	4	DRB1*13:01 [50]
	in silico prediction (percentile)	61	63	68	41	47	23	59	15	40.5	13	63		DRB4 [51]
	responding patients	1/6	2/3	2/4	‐	5/8	‐	‐	1/3	0/1	‐	1/7
	HLA restriction references		[51]
75 SASFSTFKCYGVSPT aa371‐385	in vitro binding capacity (IC50)	5286	> 40000	3329	559	519	4671	117	626	11462	> 40000	711	5
	in silico prediction (percentile)	42	94	39	17	18	53	24	40	49	86	13
	responding patients	5/6	0/3	0/4	‐	5/8	‐	‐	2/3	1/1	‐	3/7
	HLA restriction references											[50]
91 YLYRLFRKSNLKPFE aa451‐465	in vitro binding capacity (IC50)	7365	> 40000	590	543	575	23	13	4.2	323	8567	1.7	8	DRB1*11:04, DRB3 [51]
	in silico prediction (percentile)	22	26	17	11	3.1	5.1	13	1.2	5.95	11	5.3
	responding patients	3/6	1/3	0/4	‐	4/8	‐	‐	2/3	0/1	‐	1/7
	HLA restriction references								[51]
163 KPSKRSFIEDLLFNK aa811‐825	in vitro binding capacity (IC50)	> 40000	1498	451	3442	1933	3414	519	301	3981	> 40000	6806	3	DQB1*02:02, DQB1*05:03 [50]
	in silico prediction (percentile)	75	19	48	30	59	81	61	76	37.5	75	70
	responding patients	6/6	2/3	4/4	‐	4/8	‐	‐	2/3	0/1	‐	6/7
	HLA restriction references
164 SFIEDLLFNKVTLAD aa816‐830	in vitro binding capacity (IC50)	4353	3227	1098	2167	3958	15214	1298	13221	537	174	3172	2	DRB1*14:01, DQB1*05:03 [50]
	in silico prediction (percentile)	26	17	8.8	23	41	24	43	31	8.25	18	37
	responding patients	6/6	3/3	3/4	‐	5/8	‐	‐	2/3	0/1	‐	6/7
	HLA restriction references		[50]							[50]
167 AGFIKQYGDCLGDIA aa831‐845	in vitro binding capacity (IC50)	1105	> 40000	836	950	740	22262	1558	3746	16980	> 40000	716	4	DQB1*05:03 [50]
	in silico prediction (percentile)	19	83	60	55	69	61	56	71	71	59	26
	responding patients	5/6	0/3	2/4	‐	3/8	‐	‐	1/3	0/1	‐	4/7
	HLA restriction references
180 IPFAMQMAYRFNGIG aa896‐910	in vitro binding capacity (IC50)	58	11726	443	1608	25	553	7.9	23	2.2	13705	192	8	DRB1*14:01, DQB1*04:02, DQB1*05:03 [50]
	in silico prediction (percentile)	3.7	14	26	30	26	25	31	20	7	15	9.1		DRB1*11:04, DRB5 [51]
	responding patients	5/6	1/3	0/4	‐	5/8	‐	‐	1/3	0/1	‐	3/7
	HLA restriction references	[51]							[51]	[50]		[50]