Short Report

Hepatitis B virus subgenotypes D1 and D3 are prevalent in Pakistan

Saeeda Baig¹ , Anwar Siddiqui² , Runu Chakravarty³ and Tariq Moatter⁴

¹Department of Biochemistry, Ziauddin Medical College, Ziauddin University, Karachi, Pakistan

²Department of Biological and Biomedical Sciences, Juma Building, Aga Khan University, Karachi, Pakistan

³ICMR Virus Unit, ID & BG Hospital Campus, Kolkata, West Bengal, India

⁴Department of Molecular Pathology Juma Building, Aga Khan University, Karachi, Pakistan

author email corresponding author email

BMC Research Notes 2009, 2:1doi:10.1186/1756-0500-2-1

Published:	4 January 2009

Abstract

Background

As the hepatitis B genotyping is important for assessing its clinical implications and geographical distribution, the sub-genotypes have been found useful for determination of specific genomic markers related to hepatocarcinogenesis. In Pakistan, there is no reported data on molecular evolutionary analysis of HBV. A study was, therefore, much needed to evaluate the spectra of mutations present in the strains prevalent here.

Findings

to confirm specificity of PCR typing, phylogenetic analysis of the pre-S1 region and the divergence was studied through 13 sequences of 362 bp (accession number EF432765 – EF432777). A total of 315 serum samples, selected from HBsAg positive patients representing the major ethnic groups, residing in Karachi, Sindh were tested for genotyping. Genotype D (219/315) was found to be the most prevalent (70%) amongst our patients. The rest of the genotypes A and a mixture of A and D (AD) were distributed as 20%, and 10% respectively. Phylogenetic tree demonstrated clustering of 11 samples with subgenotype D1 sequences and the remaining two strains on a branch within D3 samples. All samples intermixed with strains from other countries and were found to be closely related to Indian, Iranian and Egyptian HBV strains with 98.7 – 99.0% homology.

Conclusion

This study confirms the predominance of genotype D in southeastern Asia and presence of subgenotypes DI and D3 in the Pakistani infected patients. More studies are required to investigate the reason for fewer inclusions of D3 compared to the D1 in Pakistani HBV strains.