African Journal of

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12291

Full Length Research Paper

Sequence comparison and phylogenetic analysis of core gene of hepatitis C virus from Pakistani population

Yasir Waheed#*, Sadia Tahir#, Tahir Ahmad and Ishtiaq Qadri   # These authors contributed equally to this work.
National University of Sciences and Technology (NUST) Center of Virology and Immunology, H-12 Sector, Islamabad, Pakistan.
Email: [email protected]

  •  Accepted: 21 June 2010
  •  Published: 31 July 2010


In Pakistan, more than 10 million people are living with hepatitis C virus (HCV) with high morbidity and mortality. The aims of the present study are to report HCV core gene sequences from Pakistani population and perform their sequence comparison/phylogenetic analysis. The core gene of HCV has been cloned from six different patients and sequences submitted at the National Center of Biotechnology Information (NCBI). Nucleotides and deduced amino acid sequence comparison of six isolates was performed with each other and with two HCV genotype 3a type examples reported from Japan. Phylogenetic tree of HCV core sequences was constructed using CLC software. Nucleotides sequence comparison showed that our sequences have 94 to 96% homology with NZL1 strain and 90 to 93% homology with HCV-K3A/650 strain. Deduced amino acid sequence comparison showed that our sequences have 92 to 98% homology with NZL1 strain and 88 to 94% homology with HCV-K3A/650 strain. Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and phylogenetic analysis showed that our isolates have high homology with Japanese isolates.


Key words: Hepatitis C virus, core, phylogenetic analysis, Pakistan.


HCV, Hepatitis C virus; NLS, nuclear localization signals; ER,endoplasmic reticulum; EDTA, ethylenediaminetetraacetic acid; cDNA,complementary DNA; X-Gal, bromo-4-chloro-3-indolyl-b-D-galactopyranoside;IPTG, isopropyl β-D-1-thiogalactopyranoside; DTCS, dye terminator cycle sequencing; PCR, polymerase chain reaction.