Hepatitis B virus genotypes, subgenotypes, precore, and basal core promoter mutations in the two largest provinces of Pakistan

Hepatitis B virus (HBV) genotyping has been done in most countries, but unfortunately, in Pakistan, HBV genotypic distribution is still unclear. The aim of the present study was to determine the prevalent genotype and subgenotype in the two most populated provinces in Pakistan: Punjab and Sind. In total, 236 HBV DNA-positive samples were selected for genotyping by polymerase chain reaction-restriction fragment length polymorphism (RFLP). The RFLP results were further confirmed with whole genome and partial genome sequencing. Genotype D was detected as the most prevalent (93.22%) genotype in all eight cities of both provinces; genotype C was present in 5.93% and genotype A was present in 0.85% of the samples. The D1 subtype was present in 84%, and D2 was present in 8% of 25 whole genome-sequenced samples. The C2 subtype was detected in 58.33% of S gene-sequenced samples, while D1 was detected in the remaining 41.67% of 24 samples sequenced for the S gene. Subtype D1 is the most dominant in D, while C2 is dominant in genotype C. Eight- and 15-bp deletion mutations were also detected in genotype D samples. Other precore and basal core promoter (BCP) mutations included T1915 (100%), A1679 (86.96%), T1762 (39.13%), and A1764 (30.43%), which were also detected in the genotype D samples. Genotype D subtype D1 is the most prevalent HBV strain in Pakistan with 8-bp deletion mutants the most common in HBV carriers.