Molecular characterisation of the genotypes and mutants of hepatitis B virus from South Africa

Abstract

Genotypes A, D and E of hepatitis B virus (HBV) circulate in southern Africa. The prevalence of subgenotype A1, a segment of genotype A, and its high mean nucleotide divergence suggest that this subgenotype is endemic in South African blacks. We have fully characterised subgenotype A1 sequences and identified mutations or variations that could account for the high HBeAg-negativity and low HBV DNA levels, seen in carriers of the virus. These mutations or variations can reduce HBeAg expression at three levels. Firstly, at the transcriptional level, the core promoter mutations 1762^T 1764^A, highly prevalent in isolates from hepatocellular carcinoma (HCC) patients reduce HBeAg expression. Secondly, at the translational level, mutations at 1809-1812 that alter the Kozak sequence of the precore/core open reading frame are stable traits of subgenotype A1 and affect HBeAg expression, at a level comparable to 1762^T 1764^A. The presence of 1762^T 1764^A, together with 1809-1812 mutations, reduced HBeAg expression in an additive manner. Thirdly, a G to T transversion at 1862 of the precore region affects HBeAg expression at the post-translational level, by interfering with signal peptide cleavage. Unique sequence alterations in the transcriptional regulatory elements and the HBV polymerase coding region were found in subgenotype A1. These, together with the mutations affecting HBeAg expression, may contribute to the pathogenesis of HBV-induced HCC, which has a high incidence in southern African blacks. In fact, we have shown a 4.5-fold increased risk of HCC in HBV carriers infected with genotype A, which is entirely attributable to subgenotype A1.