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Phylogenetic analysis of HDV isolates from HBsAg positive patients in Karachi, Pakistan

Shadab Perveen1, Muhammad Israr Nasir2, Syed M Shahid1, Abid Azhar1 and Obaid Yusuf Khan3*

Author Affiliations

1 The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan

2 Dow University of Health Sciences (DUHS), Karachi, Pakistan

3 Department of Genetics, University of Karachi, Karachi, Pakistan

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Virology Journal 2012, 9:162  doi:10.1186/1743-422X-9-162

Published: 15 August 2012



In spite of a high occurrence of Hepatitis Delta in the province of Sindh in Pakistan, no genetic study of Hepatitis Delta virus (HDV) isolates from this region was carried out. The aim of this study is to analyze the genetic proximity within local HDV strains, and relationship with other clades of HDV, using phylogenetic analysis.


Phylogenetic analysis of nucleotide sequences of the Hepatitis Delta Antigen (HDAg) R0 region obtained in this study, showed considerable diversity among the local strains with a potential subgroup formation within clade I. The multiple sequence alignment of predicted amino acids within clade I showed many uncommon amino acid substitutions within some conserved regions that are crucial for replication and assembly of HDV.


The studied strains showed a range of genetic diversity within HDV clade I. There is clustering of sequences into more than one group, along with formation of potential subgroup within clade I. Clustering shows the genetic closeness of strains and indicates a common origin of spread of HDV infection. Further phylogeny-based studies may provide more information about subgroup formation within clade I and may be used as an effective tool in checking and/or preventing the spread of hepatitis D virus infection in this region.

Hepatitis D virus; HDV- clades; Phylogeny; HDAg