HCV-NS5A region and response to pegylated-interferon alpha plus ribavirin therapy: mutational analyses in patients with chronic HCV infection

Objectives: Mutations in NS5A region of HCV genome have been shown to mediate IFN α resistance in few instances other than genotype 1. This study was planned to analyze NS5A sequences from patients infected with HCV 3 and 1. Methods: Forty patients positive for HCV antibodies and HCV RNA, who were on the pegylated-IFN-α and ribavirin therapy, were studied. Blood samples were collected before and after therapy. Genotyping was done by restriction fragment length polymorphism. Biochemical profile was measured before and after therapy. Pre and post-treatment quantitative detection of HCV RNA was performed by real-time PCR. Direct and nested-PCR for amplification of genotype-1 and genotype-3 was done. Sequencing was performed by Sanger dideoxy method. Phylogenetic tree of HCV NS5A region sequences were constructed. Secondary structure of NS5A region of HCV was predicted. Results: Twenty-five patients responded to therapy, while 15 did not. Twenty seven and 13 patients were found to be infected with genotype 3 and 1 respectively. SGOT and SGPT showed significant difference between responders and non-responders. Thirteen and 27 patients were infected with HCV genotype 1 and 3 respectively. Base line viral load was more in non-responders as compared to responders. Genotype 3 was more responsive to therapy. Significant difference between no. of mutations in responders and non-responders was observed in NS5A-PKRBD and extended V3 region. Changes were found in secondary structure of NS5A region. Conclusions: Knowledge of HCV genotype, presence of mutations in NS5A region and secondary structure changes are essential for predicting outcome of therapy.