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Open Access Short report

The first complete genome sequence of HCV-1a from Pakistan and a phylogenetic analysis with complete genomes from the rest of the world

Abrar Hussain12 and Muhammad Idrees1*

Author Affiliations

1 Division of Molecular Virology & Molecular Diagnostics, National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore 53700, Pakistan

2 Department of Biotechnology and Informatics, BUITEMS, Quetta, Pakistan

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Virology Journal 2013, 10:211  doi:10.1186/1743-422X-10-211

Published: 27 June 2013

Abstract

Background

Here, we report the first patient derived hepatitis C virus (HCV) complete genome from Pakistan as is not available from this region of the world.

Findings

Comprehensive evolutionary and phylogenetic analyses were conducted. The comparison was made in order to identify evolutionary and molecular phylogenetic relationships among HCV strains belonging to genotype 1a. The evolutionary divergence analysis for nucleotide and amino acid sequences, conducted by equal input model, suggested that evolutionary nucleotide and amino acid distances showed that the HCV Pakistani strain was genetically far from Denmark strain (0.29400 nt, 0.819646 aa) and near to German strain (0.06557 nt, 0.139449 aa), respectively.

Conclusion

The current study will help to understand phylogenetic relationship of circulating Pakistani isolates.

Keywords:
HCV genotype 1a; Complete genome comparison; Evolutionary and Phylogenetic