Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of HCV NS5B Protein. [10.5812/hepatmon.6142]

作者：Yasir Waheed, Umar Saeed, Sadia Anjum, Muhammad Sohail Afzal, Muhammad Usman Ashraf · 发表于：Hepatitis Monthly · 年份：2012 · DOI：10.5812/hepatmon.6142 · 被引用次数：38 · 研究领域：Hepatitis C virus research、vaccines and immunoinformatics approaches、Monoclonal and Polyclonal Antibodies Research

BACKGROUND: Hepatitis C virus (HCV) is a plus stranded RNA virus which encodes 10 different genes. The HCV NS5B gene encodes a polymerase, which is responsible for the replication of the virus and is a potential target for the development of antiviral agents. HCV has a high mutation rate and is classified into six major genotypes. OBJECTIVES: The aim of this study was to draw a representing consensus sequence of each HCV genotype, align all six consensus sequences to draw a global consensus sequence and also study the highly conserved residues. MATERIALS AND METHODS: 236 HCV NS5B sequences, belonging to all six genotypes, reported from all over the world were aligned then a representing phylogenetic tree wasdrawn. RESULTS: The active site residues D220, D225, D318 and D319, which bind the divalent cations, are highly conserved among all the HCV genotypes. The other catalytic pocket residues, R158, S367, R386, and T390 and R394, which interact with the triphosphate of NTPs, are also highly conserved while T390 is mutated to valine in the genotype 5. The motif B residues G283, T286, T287 and N291, which take part in sugar selection by RdRp, are also highly conserved except for T286 which is mutated to proline in the genotypes 3 and 6. The residues E18, Y191, C274, Y276 and H502, which take part in primer/template interaction, are also high conserved except for H502 which is mutated to serine in genotype 2. High variation in all the six consensus sequences was observed in a 12 a...