Table 1. In vivo isolated, highly scored EBV-specific candidate-epitopes–in silico predicted results and IFN-γ EliSpot-based screening for immunogenicity.

Sequence	Origin	Abbreviation	Epstein-Barr-Virus-Protein	Peptide-Ion-Score	NetMHC 4.0		NetCTL 1.2		NetMHCstab 1.0		ExPASy-ProtParam tool		SYF-PEITHI	Responders
[aa]	[B-LCL]		[UniProtKB-Database]	[pep_score]	[%Rank]	[BL]	[score]	[E]	[score]	[BL]	[Instab.- Index]	[class.]	[score]	[IFN-γ EliSpot (day 7)]
RLRAEAQVK		A*03_EBNA3ARLRA	Ebstein-Barr-Nuclear-Antigen-3A–EBNA-3A		0.40	SB	1.4208	E	0.633	SB HS	18.71	stable	36	9/18
KLLRYASAK	in vivo [024]	A*03_BPLF1KLLR	Large tegument protein deneddylase–BPLF1	13.57	0.01	SB	1.6755	E	0.785	SB HS	38.79	stable	35	5/14
TVARHLLGAK	in vivo [623]	A*03_BALF5TVAR	DNA polymerase catalytic protein - BALF5	13.30	0.15	SB	0.7951	E	0.586	SB WS	19.77	stable	26	7/14
ATGMVPAVKK	in vivo [623]	A*03_BBRF1ATGM	Portal protein UL6 homolog–BBRF1	28.73	0.20	SB	0.9726	E	0.431	WB	36.15	stable	20	2/10
KLVCSEPLVK	in vivo [024, 623]	A*03_BcRF1KLVC	TBP-like protein - BcRF1	30.29	0.40	SB	0.9152	E	0.597	WB WS	36.15	stable	31	5/14
VTLAHAGYY	in vivo [1335]	A*03_BILF2VTLA (1),(2)	Glycoprotein–BILF2	49.38	0.70	WB	1.2361	E	0.419	WB	–5.70	stable	14	13/21
FLLAMTSLR	in vivo [623]	A*03_BcRF1FLLA (1),(2)	TBP-like protein–BcRF1	12.90	0.70	WB	1.4480	E	0.347	WB	27.09	stable	21	13/19
FLGKYIKVKK	in vivo [024]	A*03_BTRF1FLGK	„uncharacterized protein“–BTRF1	16.21	1.00	WB	1.1954	E	0.357	WB	–19.35	stable	24	5/10
QVATEGLAK	in vivo [024]	A*03_BALF3QVAT (1),(2)	Tripartite terminase subunit UL28 homolog–BALF3	18.17	1.20	WB	0.9267	E	0.414	WB WS	21.91	stable	30	12/19
TLVDVRAIK	in vivo [623]	A*03_BaRF1TLVD	Ribonucleoside-diphosphate reductase small chain–BaRF1	16.60	1.20	WB	1.0387	E	0.415	WB	–17.24	stable	26	5/14
KIVTNILIY	in vivo [024]	A*03_gBKIVT	envelope glycoprotein B–gB	10.09	1.30	WB	1.2615	E	0.346	WB	34.11	stable	20	2/10
LIIPNVTLAH	in vivo [1335]	A*03_BILF2LIIP(2)	Glycoprotein–BILF2	49.38	4.00		0.7476		0.239		–10.86	stable	22	11/20

[aa] = amino acid, [B-LCL] = B-lymphoblastoid cell line, ⁽¹⁾ = component of EBV_Consensus+3P_MIX, ⁽²⁾ = component of EBV_Consensus+4P_MIX, [Ref.] = References, [pep_score] = peptide score (sequences’ probability of an existent match to a database entry), [BL] = Binding Level, [SB] = strong binder, [WB] = weak binder, [HS] = highly stable binder, [WS] = weakly stable binder, [score] = combined prediction score, [E] = identified as potential CTL epitope, [Instab.-Index] = Instability Index, [class.] = classification.

Overview of the eleven investigated HLA-A*03:01-restricted candidate-epitopes and the known A*03_EBNA3A_RLRA as reference epitope regarding their peptide sequences, origin, protein source, analyzed prediction scores (NetMHC 4.0, NetCTL 1.2, NetMHCstab 1.0, ExPASy-ProtParam tool, SYFPEITHI) and in vitro T-cell responses (IFN-γ EliSpot assay). All isolated sequences with a peptide-ion-score >10 [pep_score] that reached the highest scores in the subsequent predictions regarding their peptide-binding affinity and peptide-MHC complex stability as well as with a clinically relevant role in EBV-latency, -reactivation and/or potentially malignant transformation are included. Candidate-epitopes were classified as immunodominant (immunoresponse in ≥20% of donors) and highly immunodominant (immunoresponse in >50% of the donors, as typed in bold) assessed by in vitro IFN-γ EliSpot assay.