Protective efficacy of multiepitope vaccines constructed from common antigens of Eimeria species in chickens

Chen, Chen; Su, Junzhi; Lu, Mingmin; Xu, Lixin; Yan, Ruofeng; Li, Xiangrui; Song, Xiaokai

doi:10.1186/s13567-023-01253-y

Veterinary Research

Table 1 Bioinformatics analysis of four common antigens.

From: Protective efficacy of multiepitope vaccines constructed from common antigens of Eimeria species in chickens

Gene	Fragment	Size (aa)	Prediction of the binding site to MHC I							Prediction of the binding site to MHC II
Gene	Fragment	Size (aa)	Allele	Position	Epitope	Score (aff)	IC50 (nm)	%Rank^a	Binding Level^b	Allele	Position	Epitope	Core	Score-EL^c	%Rank-EL^d	Score-BA^e	%Rank-BA^f
14-3-3	14	149 (95–243)	HLA-B40:06	178	AELPSTHPI	0.511	198.69	0.15	≤ SB	DRB1-1310	145	YYRYISEFSNEEGKK	YISEFSNEE	0.659719	0.87 (SB)	0.368476	2.88
			HLA-B40:06	178	AELPSTHPI	0.511	198.69	0.15	≤ SB		144	DYYRYISEFSNEEGK	YISEFSNEE	0.575921	1.50 (SB)	0.351085	4.26
			HLA-B41:03	178	AELPSTHPI	0.668	36.31	0.12	≤ SB		143	GDYYRYISEFSNEEG	YRYISEFSN	0.555038	1.72 (SB)	0.336931	5.73
			HLA-B41:03	178	AELPSTHPI	0.668	36.31	0.12	≤ SB	DRB1-1366	145	YYRYISEFSNEEGKK	YISEFSNEE	0.518796	1.27 (SB)	0.388953	11.89
			HLA-B41:04	178	AELPSTHPI	0.678	32.48	0.05	≤ SB	DRB1-1445	95	NKALAASYRQKVENE	LAASYRQKV	0.663603	0.22 (SB)	0.346217	4.48
			HLA-B41:04	178	AELPSTHPI	0.678	32.48	0.05	≤ SB	DRB1-1482	95	NKALAASYRQKVENE	LAASYRQKV	0.792532	0.13 (SB)	0.511766	2.99
EF2	E	177 (387–563)	HLA-B40:06	524	GELHVEICL	0.372	888.54	0.80	≤ WB	DRB1-1310	476	SPVVRVAVKPKDMKE	VRVAVKPKD	0.895005	0.05 (SB)	0.368398	2.88
										DRB1-1310	541	QIDIIVSDPVVSYRE	IVSDPVVSY	0.577648	1.48 (SB)	0.399450	1.37
										DRB1-1366	476	SPVVRVAVKPKDMKE	VRVAVKPKD	0.855490	0.06 (SB)	0.419370	7.71
			HLA-B41:03	524	GELHVEICL	0.591	83.09	0.50	≤ SB	DRB1-1366	541	QIDIIVSDPVVSYRE	IVSDPVVSY	0.527570	1.21 (SB)	0.523473	1.06
			HLA-B41:03	524	GELHVEICL	0.591	83.09	0.50	≤ SB	DRB1-1445	476	SPVVRVAVKPKDMKE	VRVAVKPKD	0.756613	0.04 (SB)	0.312353	8.66
			HLA-B41:04	524	GELHVEICL	0.457	356.37	0.80	≤ WB	DRB1-1445	541	QIDIIVSDPVVSYRE	IVSDPVVSY	0.704201	0.10 (SB) 0.453546 0.29	0.453546	0.29
										DRB1-1482	476	SPVVRVAVKPKDMKE	VRVAVKPKD	0.763648 0.785701	0.19 (SB) 0.14(SB)	0.432076	12.81
										DRB1-1482	541	QIDIIVSDPVVSYRE	IVSDPVVSY	0.785701	0.14 (SB)	0.600302	0.23
GAPDH	G	176 (52–227)	HLA-B40:06	138	EEYQPTLQV	0.371	902.73	0.80	≤ WB	DRB1-1310	115	AKKVIISAPPKDDTP	VIISAPPKD	0.703120	0.62 (SB)	0.318953	8.03
			HLA-B40:06	138	EEYQPTLQV	0.371	902.73	0.80	≤ WB		128	TPMFVMGVNHEEYQP	FVMGVNHEE	0.597728	1.31 (SB)	0.361971	3.35
			HLA-B41:03	138	EEYQPTLQV	0.491	247.81	1.50	≤ WB		63	DGNLVVEGKTIQVFA	LVVEGKTIQ	0.487992	2.60 (WB)	0.283325	15.25
				138	EEYQPTLQV	0.491	247.81	1.50	≤ WB	DRB1-1366	115	AKKVIISAPPKDDTP	VIISAPPKD	0.576140	0.89 (SB)	0.365268	16.19
				68	VEGKTIQVF	0.548	133.03	1.00	≤ WB	DRB1-1366	63	DGNLVVEGKTIQVFA	LVVEGKTIQ	0.475566	1.62 (SB)	0.389848	11.76
				68	VEGKTIQVF	0.548	133.03	1.00	≤ WB	DRB1-1445	63	DGNLVVEGKTIQVFA	LVVEGKTIQ	0.534977	0.87 (SB)	0.330942	6.06
			HLA-B41:04	104	KEKAGLHIS	0.355	1069.33	2.00	≤ WB		115	AKKVIISAPPKDDTP	VIISAPPKD	0.485379	1.33 (SB)	0.267099	18.43
				104	KEKAGLHIS	0.355	1069.33	2.00	≤ WB		205	GSNIIPASTGAAKAV	IIPASTGAA	0.436942	1.95 (SB)	0.320841	7.38
				68	VEGKTIQVF	0.346	1182.43	2.00	≤ WB	DRB1-1482	115	AKKVIISAPPKDDTP	VIISAPPKD	0.579515	1.13 (SB)	0.406430	18.20
				68	VEGKTIQVF	0.346	1182.43	2.00	≤ WB	DRB1-1482	63	DGNLVVEGKTIQVFA	LVVEGKTIQ	0.501950	1.91 (SB)	0.457851	8.44
Transhydrogenase	T	326 (579–904)	HLA-B40:06	646	AEVLLRVS	0.527	166.85	0.12	≤ SB	DRB1_1310	811	GDAYQRAQRELIANT	YQRAQRELI	0.701329	0.63 (SB)	0.390542	1.71
				646	AEVLLRVS	0.527	166.85	0.12	≤ SB	DRB1_1310	890	VDGITVIGRKRIETR	ITVIGRKRI	0.626872	1.10 (SB)	0.355965	3.84
				743	VEAAKVFVI	0.485	264.37	0.20	≤ SB	DRB1_1366	811	GDAYQRAQRELIANT	YQRAQRELI	0.532553	1.18 (SB)	0.444541	5.14
				743	VEAAKVFVI	0.485	264.37	0.20	≤ SB	DRB1_1366	890	VDGITVIGRKRIETR	ITVIGRKRI	0.513415	1.30 (SB)	0.462875	3.71
			HLA-B41:03	743	VEAAKVFVI	0.659	40.24	0.15	≤ SB	DRB1_1445	890	VDGITVIGRKRIETR	ITVIGRKRI	0.821916	0.00 (SB)	0.413373	0.87
											772	FGHDVRSATREEVES	VRSATREEV	0.699963	0.11 (SB)	0.275680	16.11
											811	GDAYQRAQRELIANT	YQRAQRELI	0.419602	2.23 (WB)	0.275648	16.12
			HLA-B41:04	646	AEVLLRVSA	0.602	74.56	0.15	≤ SB	DRB1_1482	890	VDGITVIGRKRIETR	ITVIGRKRI	0.872567	0.02 (SB)	0.544946	1.38
				646	AEVLLRVSA	0.602	74.56	0.15	≤ SB		772	FGHDVRSATREEVES	VRSATREEV	0.822842	0.08 (SB)	0.406524	18.18
				743	VEAAKVFVI	0.589	85.54	0.17	≤ SB		698	VPRVTRAQKLDVKSA	VTRAQKLDV	0.737749	0.27 (SB)	0.544297	1.40
				743	VEAAKVFVI	0.589	85.54	0.17	≤ SB		811	GDAYQRAQRELIANT	YQRAQRELI	0.551109	1.37 (SB)	0.446054	10.27

a, Ranking of predicted scores of selected epitopes among a group of 200 000 random natural 9 aa short peptides. b, Determination of the binding strength between selected epitopes and MHC molecules. The selected epitopes will be identified as strong binders (SBs) if %Rank < 0.5 or IC50 < 50. The selected epitopes will be identified as weak binders (WBs) if 0.5 < %Rank < 2 or 50 < IC50 < 500. c, Predictiveness scores of the screened epitopes. d, In a group of random natural peptides, the percentile rank of the predictiveness scores of the screened epitopes. The selected epitopes will be identified as strong binders (SBs) if %Rank-EL < 2. The selected epitopes will be identified as strong binders (SBs) if 2 < %Rank-EL < 5. e, The predicted binding affinity in log-scale (printed only if binding affinity predictions were selected). f, percentile rank of predicted affinity compared to a group of 100 000 random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities (printed only if binding affinity predictions were selected).

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ISSN: 1297-9716

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