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

Table 2 The sequences of the chosen epitopes were compared to the consensus sequence and conservation scores (as percentages) were calculated

CLASS I EPITOPE	Consensus Epitope sequence	HCV GENOTYPES						Mean across genotypes	MAX.	MIN.	SD	p-value
		1	2	3	4	5	6
NS3^1073-1081	CINGVMWTV	78	67	67	67	78	67	70.67	67	78	5.680	0.3062
NS3^1406-1415	LTSLGLNAV	67	56	67	78	67	56	65.17	56	78	8.280	0.1645
NS4^1807-1816	LLFNILGGW	100	78	78	100	100	78	89.00	78	100	12.049	0.6513
NS4^1851-1859	ILAGYGAGV	89	67	89	78	89	67	79.83	67	89	10.815	0.2231
NS5B^2422-2433	MSYSWTGAL	89	89	89	100	89	67	87.17	67	100	10.815	0.406
NS5B^2727-2735	GLRDCTMLV	78	56	44	78	78	33	61.17	33	78	19.823	0.4142
	Mean within genotypes	83.50	68.83	72.33	83.50	83.50	61.33
CLASS II EPITOPE	Consensus Epitope sequence	1	2	3	4	5	6	Mean across genotypes	MAX.	MIN.	SD	p-value
CORE^17-40	RRPQDVKFPGGGQIVGGVYLLPRR	100	96	66	96	96	96	91.67	67	78	5.680	0.3062
NS3^1248-1261	GYKVLVLNPSVAAT	100	93	93	100	100	93	96.50	93	100	3.834	0.32
NS3^1781-1800	LPGNPAVASLMATAAVTSP	85	80	95	85	90	65	83.33	65	95	10.327	0.4142
NS4^1801-1820	LTTSQTLLFNILGGWVASQL	85	65	80	90	85	70	79.17	65	90	9.703	0.962
NS5B^2571-2590	KGGRKPALIVYPDLGVRVC	80	80	90	95	95	80	86.67	80	95	7.527	0.2231
NS5B^2661-2680	QCCDLEPEARVAIKSLTERL	85	55	70	80	60	50	66.67	50	85	14.023	0.4159
	Mean within genotypes	89.17	78.17	82.33	91.00	87.67	75.67

ISSN: 1471-2172