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 3 Binding affinity scores of published 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 (A02)**	CINGVCWTV	1a		17802	67	61	14908	15501	12611	23637	20927	25523	19827	13679	19257	23485
1073-1081	CVNGVCWTV	1b		16997	110	20	12228	13122	11766	21885	15696	13382	18288	12132	20367	23007
	SISGVLWTV	2a variant		18961	11	16	21483	11417	11417	22455	22186	29702	18590	15055	15691	20667
	TVGGVMWTV	3a		19940	64	8	12677	14750	9776	20729	21877	24623	16182	18054	26500	24303
	AVNGVMWTV	4a variant		17734	23	14	24001	4015^#	12036	10753	20258	20595	17093	12996	13641	18882
	CINGVLWTV	5a		15172	26	39	17548	13613	13865	23524	21854	15854	18628	11203	17516	21090
	CINGVMWTL	5a variant		17922	140	101	10449	14413	11435	18947	13165	11237	2239	13165	13572	19956
*NS3 (A02)**	KLVALGINA	1a		22719	273	15048	32261	1830	18800	24242	25216	37253	23529	20557	4839	19019
1406-1415	KLSGLGLNA	1b		19133	475	21824	33559	2557	13152	20740	27147	37083	23891	19220	8973	18099
	QLTSLGLNA	4a		20013	7051	15292	33674	12859	12517	26454	24440	37244	22168	26218	7165	19904
	KLVALGINAV	1a		37929	52	8564	39134	NO VALUE	31977	19547	42247	34339	NO VALUE	NO VALUE	NO VALUE	26021
	LTGLGINAV	5a		12100	5692	304	32426	10980	20519	21309	20981	33652	25012	21599	12577	26332
	QLTGLGINA	5a variant		22408	6972	7419	34672	13389	17488	26117	23541	36968	25569	22283	15466	20054
*NS4B (A02)**	LLFNILGGW	1a, 1b, 4, 5a		22942	14359	17095	18086	17906	9175	24903	19854	17154	956^#	962^#	5918	23118
1807-1816	MFFNILGGWV	3a		24613	23482	19706	343	15640	1707^#	21757	11817	8151	10769	1251	13832	26621
	LLFNILGGWV	1a, 1b, 4, 5a		32231	44	1159^#	38969	NO VALUE	19453	32445	40287	25767	NO VALUE	NO VALUE	NO VALUE	25868
*NS4B (A02)**	ILAGYGAGV	1a, 1b, 5a		20500	15	530^#	30882	15492	10120	11883	21134	37213	22934	20702	3735	20143
1851-1859	ILAGYGTGV	5a variant		20351	18	193	32028	17493	12563	11272	21994	36657	23555	20603	2196	19849
*NS5B (B15)**	MSYSWTGAL	1a, 1b, 4		12612	1522	24	2924	2372	5457	1530^#	50	8456	10166	523^#	80	16876
2422-2433	MSYTWTGAL	5a		12133	2640	22	8602	2141^#	7606	2515^#	58	9150	10680	787^#	144	17267
	YTWTGALIT	5a variant		15779	3000	13286	33166	13737	1561	18979	3920	27619	22480	17360	6553	18765
*NS5B (A02)**	GLQDCTMLV	1a		18371	8	5733	11972	13187	6275	20996	27015	35681	25282	22002	10687	17601
2727-2735	KLQDCTMLV	1b		17735	7	3878	6160	2071^#	9527	17308	26776	35038	23310	18296	3587	16634
	KLRDCTLLV	5a		19744	13	14912	15150	10	5150	2800	27145	36627	21481	20362	1720^#	18071
	ALRDCTMLV	4a		19976	19	4673	19836	29	9982	5384	26302	36740	24190	22343	1206^#	20027

<50 IC₅₀nm, bold, high affinity.
>50 IC₅₀nm, <500 IC₅₀nm, italic, intermediate affinity.
>500 IC₅₀nm, #, poor affinity.
No value indicates server produced no binding score.

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ISSN: 1471-2172

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