Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Protein


Yasir Waheed 1 , * , Umar Saeed 1 , Sadia Anjum 1 , Mohammad Sohail Afzal 1 , Muhammad Ashraf 1

1 Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), [email protected], (44000), Pakistan

How to Cite: Waheed Y , Saeed U , Anjum S , Afzal M , Ashraf M . Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Protein, Hepat Mon. Online ahead of Print ; 12(9):6142. doi: 10.5812/hepatmon.6142.


Hepatitis Monthly: 12 (9); 6142
Published Online: September 30, 2012
Article Type: Research Article
Received: May 13, 2012
Accepted: August 14, 2012


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 amino acid beta hairpin loop, which interacts with the double stranded RNA. Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine. The HCV NS5B phylogenetic tree shows the clusters of different genotypes and their evolutionary association.

Conclusions: In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved. These are target sites for the development of antiviral agents or peptide vaccines. The phylogenetic analysis suggests that different HCV genotypes have been evolved from the genotype 1a.

Full Text

Full text is available in PDF

© 2012, Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.