Distinct mutant hepatitis B virus genomes, with alterations in all four open reading frames, in a single South African hepatocellular carcinoma patient

Sequence variation of hepatitis B virus (HBV) can influence the replication, antigen expression and pathogenicity of the virus. We report on the mutational analysis of HBV performed in a 28-year-old Black South African female diagnosed with HBV-induced hepatocellular carcinoma. Full-genome amplification and DNA sequencing of HBV was carried out. Five distinct complete genomic clones were described with extensive genomic and intragenic variation. Phylogenetic analysis revealed that all five clones belonged to subgenotype A1 and that there were at least four virus populations with genomes of different lengths ranging from 3194 to 3253 base pairs. In this particular patient, four major characteristic features, not previously reported to occur simultaneously in HBV isolated from a single patient, were observed. Firstly, all the clones harboured a 13 base pair deletion and a 45 base pair insertion in the basic core promoter (BCP). Secondly, a 37 base pair insertion in the core gene with three adjacent single nucleotide deletions were observed. Thirdly, premature S gene stop codons were observed in some clones and lastly X gene initiation codon mutations were also observed. The complex nature of the mutations in the HBV isolated from this single patient may have contributed to the early onset of hepatocarcinogenesis.