Natural epitope variants of the hepatitis C virus impair cytotoxic T lymphocyte activity

Table 2 Nonsynonymous and synonymous mutations in different regions of HCV NS3

Region (aa)	Length (bp)	PCR cycles	No. of clones	Mutation		P	Mutation
				Expected sporadic	NSY		SYN	NSY/ SYN
1060-1069	30	70	90	0.25	1	> 0.050	0	1/0
1070-1079	30	70	90	0.25	5	< 0.001	3	5/3
1080-1089	30	70	90	0.25	4	< 0.001	0	4/0
1090-1099	30	70	90	0.25	3	< 0.001	5	3/5
1100-1109	30	70	90	0.25	5	< 0.001	0	5/0
1110-1119	30	70	90	0.25	3	< 0.001	1	3/1
1120-1129	30	70	90	0.25	1	> 0.050	1	1/1
1130-1139	30	70	90	0.25	4	< 0.001	0	4/0
1140-1149	30	70	90	0.25	0	NS	0	0
1150-1159	30	70	90	0.25	4	< 0.001	0	4/0
1160-1169	30	70	90	0.25	0	NS	0	0
1170-1179	30	70	90	0.25	3	< 0.001	2	3/2
1180-1189	30	70	90	0.25	6	< 0.001	0	6/0
1190-1198	27	70	90	0.23	0	NS	0	0
1073-10811	27	70	90	0.23	4	< 0.001	2	4/2
1131-11391	27	70	90	0.23	4	< 0.001	0	4/0
1169-11771	27	70	90	0.23	3	< 0.001	2	3/2

¹Epitope region. Expected sporadic mutations = ER × L × Nc × N × P/Ns, where ER = error rate of polymerases (2.02 × 10^-6), L: Nucleotide length of compared region; Nc: Number of PCR cycles; N: Number of clones sequenced; P: Proportion of sporadic mutations expected to produce amino acid substitutions (2/3), Ns: Number of sample (1) according to Smith et al[37] (1997). PCR: Polymerase chain reaction; NS: No significant.