Identification of hepatitis C virus (HCV) subtype 1b strains that are highly, or only weakly, associated with hepatocellular carcinoma on the basis of the secondary structure of an amino-terminal portion of the HCV NS3 protein

Abstract

The NS3 protein of hepatitis C virus subtype 1b (HCV-1b) isolates obtained from 89 patients with hepatocellular carcinoma (HCC) and 78 patients without HCC were analyzed. On the basis of the secondary structure of the amino-terminal 120 residues of NS3, HCV-1b isolates were classified into group A, group B, and an indeterminate group, each of which was further divided into a number of subgroups, such as A1-1, A1-2, A2-1, A2-2, B1-1, B1-2, B2-1, B2-2, C-1, C-2, and C-3. HCV-1b isolates of subgroup B1-1 were found in 53 (59.6%) of 89 patients with HCC and 19 (24.4%) of 78 patients without HCC, with the difference between the two patient groups being statistically significant (P < 0.00001). Although the number of isolates was small, subgroup B2-1 was also highly associated with HCC, with all five isolates in that subgroup being found in patients with HCC (P < 0.05). On the other hand, HCV-1b isolates of subgroup A1-1 were associated only weakly with HCC; they were found in 6 (6.7%) of 89 patients with HCC and in 25 (32.1%) of 78 patients without HCC, with the difference between the two patient groups being statistically significant (P < 0.0001). The other subgroups, such as A1-2, A2-1, B1-2, C-1, C-2, and C-3, were moderately associated with HCC; their distribution patterns among patients with HCC did not differ significantly from those among patients without HCC. Taken together, our results suggest that HCV-1b isolates of subgroups B1-1 and B2-1 are highly associated with HCC and that this secondary structure analysis may be useful for predicting the relative risk of developing HCC.

FIG. 1.

Schematic representation of secondary structure of the amino-terminal 120 residues of NS3 of HCV-1b isolates obtained from patients with and without HCC. (A) Representative forms of group A, which can be further classified into subgroups A1-1, A1-2, A2-1, and A2-2, based on the number and positions of turn structures; (B) representative forms of group B, which can be further classified into subgroups B1-1, B1-2, B2-1, and B2-2; (C) representative forms of an indeterminate group, which can be further classified into subgroups C-1, C-2, C-3, C-etc. The looped, zigzag, straight, and bent lines represent α-helix, β-sheet, coil, and turn structures, respectively. The numbers along the secondary structure indicate amino acid positions.

FIG. 2.

Sequence alignment of the amino-terminal 120 residues of NS3 of HCV-1b isolates obtained from patients with and without HCC. Representative sequences of each of the subgroups are aligned with a consensus sequence, shown on the top. Dashes indicate residues identical to the residue in the consensus sequence. The numbers along the consensus sequence indicate amino acid positions.