Molecular characterization of hepatitis B virus basal core promoter and precore region of isolates from chronic hepatitis B patients.

OBJECTIVE: To analyse mutations in precore and core promoter regions of hepatitis B virus genome in chronic hepatitis B patients. METHODS: The cross-sectional prospective study was conducted at the Centre of Biotechnology and Microbiology, University of Peshawar and Pakistan Health Research Council (PHRC), Research Centre, Khyber Medical College Peshawar from June 2014 to June 2015, and comprised samples from treatment-naïve chronic hepatitis B patients aged >15 years from three cities of Pakistan. The samples included patients who were both positive and negative for hepatitis B envelope antigen. Viral load, hepatitis B envelope antigen / anti-hepatitis B envelope status, hepatitis B virus enzyme-linked immunosorbent assay and alanine aminotransferase levels were determined. Direct sequencing of basal core promoter and precore regions of hepatitis B virus genome was carried out following a nested polymerase chain reaction approach. Phylogenetic tree was constructed using Molecular Evolutionary Genetics Analysis software version 6.0. Data was analysed using SPSS 16. RESULTS: Of the 50 patients, 33(66%) were males. The overall mean age was 28.5±11.4 years. Of all the subjects, 25(50%) each were positive and negative for hepatitis B envelope antigen. Precore stop codon mutation G1896A was detected in 19 (38%) isolates; 17(34%) among negative patients and 2(4%) in positive patients. Classic A1762T/G1764A double mutation was noted in 15(30%) isolates. Mutation at position 1764 was observed in 12(48%) samples. A rare G1764T mutation was also detected in 6(12%) isolates. The CG1802-1803 mutation was detected in 47(94%) isolates, while all the 50(100%) isolates had T1858A. The GCAC Kozak sequence was present in 43(86%) isolates; CAA1817-1819 in 49(98%); and G1888 in 49(98%). Overall, 9(18%) isolates had wild-type sequences at all important loci, including positions 1762, 1764 and 1896. The pattern of sequences at genotype specific positions and phylogenetic tree speculates that majority of study isolates belonged to genotype D. CONCLUSION: Basal core promoter and precore regions variants along with the preponderances of genotype D-specific mutations suggested a higher risk of hepatocellular carcinoma and poor clinical outcome in such patients.