Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds

Prabdial-Sing, Nishi; Puren, Adrian J; Bowyer, Sheila M

doi:10.1186/1471-2172-13-67

Table 4 Binding affinity scores of “newly predicted” epitopes and their variants were determined by the IEDB prediction program to relevant supertypes in South Africa

From: Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds

GENE	EPITOPE SEQUENCE	GENOTYPE OF EPITOPE		Class A- Alleles						Class B- Alleles
			Supertypes	A01	A02		A24	A01A03	A01A24	B07			B58		B27
			Allele type	A*01:01	A*02:01	A*68:02	A*23:01	A*30:01	A*29:02	B*07:02	B*35:01	B*53:01	B*57:01	B*58:01	B*15:03	B*27:05
NS3	LTGPTPLLY	5a, 1b		15	23679	24474	24873	4551	5	24599	6188	7688	448	28	1558^#	22842
	LHGPTPLLY	1a		10396	24884	27469	21381	17350	10	26731	12561	6443	21175	9987	442	23420
	FLSTATQTF	5a		165	15329	17845	3634	1663	1886	15839	40	17977	16320	4231	8	18662
	IVSTAAQTF	1a		20409	23323	22013	4758	11756	5496	11246	75	13372	814^#	425	55	22273
	VLSTVTQSF	1b, 2a		18550	13712	17004	4838	16940	5785	15666	988^#	29052	11492	1654	26	21745
	IVSTDTQSF	4a		19885	22289	20020	12440	14943	5300	6080	151	8229	4394	973^#	47	24757
	TLAGPKGPV	5a, 6a		23444	2081^#	13	33957	16907	18949	6657	21854	39095	25027	22108	20499	22034
	TLASPRGPV	1b		22044	1451^#	8	32375	13790	18855	2453	21660	39379	25346	22237	6235	22501
	TLASSRGPV	2a		22034	857^#	11	29481	9965	20464	2095	19022	38571	24511	22225	3353	22267
	TLASAKHPA	3a		21914	413	49	29038	10681	19694	16284	12935	39038	24637	21967	13015	23364
	TIASPKGPV	1a		22885	7397	7	34010	15054	20663	7437	19533	38620	25493	22070	16303	24145
	SVIDCNSAV	5a		21948	30	9	24435	8789	12923	1702	4571	35486	21627	21514	3381	25586
	SVTDCNTCV	1b		21476	131	24	30991	15202	21169	19345	15846	19349	26045	22021	11521	22609
	SVIDCNVAV	1b, 2a, 6a		21855	15	6	22019	7833	13308	3218	4376	31399	24317	21463	3412	24232
	SVIDCNTCV	1a		22281	25	13	23478	14812	17452	17390	13879	20769	25334	21666	7032	23918
	SVIDCNTSV	4a		22543	18	9	25166	10636	15522	3402	11164	17097	24124	20942	4646	24512
	ITYSTYGKF	1b, 5a, 2a, 2b, 1a, 4a		16829	22979	16133	124	9722	352	21954	6132	16141	354	43	27	20982
	LTYSTYGKF	3a		14296	22834	13829	263	10036	379	22076	3345	11660	860^#	41	31	20046
	KVLVLNPSV	1a, 1b, 2a, 2b, 4a, 5a, 6a		23587	50	6303	27046	21	18669	14670	21450	31145	20648	8842	3129^#	18558
	RAKAPPPSW	5a, 1b, 2a, 6a		25817	25080	27568	8387	308	25791	7172	18126	8580	31	11	596^#	22382
	RAQAPPPSW	1b, 3a, 1a		24980	24747	27454	22992	6443	24136	6017	14212	3253	38	8	1675^#	17482
	KVWLAPPPSW	4a		24000	4927	22172	26746	170	16220	18770	9620	39029	21580	20215	12296	20633
	LTSLGVNAV	5a		5815	3795	42	33629	6533	20008	16663	13886	27357	24243	18277	3860^#	24767
	LTSLGLNAV	5a variant		5305	3082	64	32917	6065	18186	16615	16431	29952	24579	19519	7004	23118

<50 IC₅₀nm, bold, high affinity.
>50 IC₅₀nm, <500 IC₅₀nm, italic, intermediate affinity.
>500 IC₅₀nm, #, poor affinity.

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ISSN: 1471-2172

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