Variation analysis of E1 and E2 in HCV subtypes

Pegylated interferon and ribavirin combination therapy effectively suppresses viral replication in 50 %-60 % of hepatitis C virus (HCV)-infected patients. However, HCV-infected patients often display varied responses to therapy, and strains of subtype lb (the most widespread HCV subtype worldwide) have more-severe clinical manifestations, greater viral loads, and poorer responses to interferon treatment. Therefore, understanding the genomic variability of HCV is crucial to treatment of HCV infection. In this study, we used the appropriate software to analyze the nucleotide, and amino acid sequences of the envelope proteins (E1 and E2) of HCV to investigate the extent of their variability in several HCV subtypes (1a, 1b, 2a, 2b, 3a, 4a, 5a and 6a) and calculated the ratio of nonsynonymous to synonymous substitutions (dN/dS) in these proteins to investigate the immunological pressure acting on them. We also predicted the N-glycosylation sites in E1 and E2 to determine their association with viral neutralization. We found that E1 is more variable, has a higher dN/dS ratio, and has more N-glycosylation sites than E2 in HCV subtype 1b. This indicates that the variability of E1, its dN/dS ratio, and its degree of N-glycosylation might play an important role in the treatment of infection with HCV subtype 1b.