Analysis of complete and partial genome sequences of hepatitis b virus and determination of its genotypes and sub-genotypes from Pakistan

Hepatitis b virus has been classified into eight genotypes from a to h which have variety in geographical distribution. hbv/d is reported to be the most prevalent genotype in pakistan. sub genotypes d1 and d3 were reported in a study from karachi. present study was designed to investigate the genotypes and sub-genotypes of hbv with sequencing of s gene fragment as well as complete viral genome of samples from islamabad,pakistan. a total of 22 hbv sample were genotyped by type specific primer pcr method. complete viral genome of 4 samples and the s gene fragment of all samples was subjected to direct sequencing. genotypes and sub-genotypes were confirmed by phylogenetic analyses of the sequences. employing type specific primer pcr method,14 (63.6%) samples were detected with hbv/d infection while a mix infection with hbv/a and hbv/d was detected in 8 (36.4%) samples. however on direct sequencing of s gene fragment,all 20 of the sequenced samples were identified as only genotype d and not genotype a or mixed,while complete genome sequences of 4 were identified as sub-genotype d1. thus this study provides evidence for prevalence of d genotype more specifically sub-genotype d1 in islamabad. furthermore,it is observed that sequence based results are more reliable as compared to type specific pcr based method.