Variability of the preC/C region of hepatitis B virus genotype A from a South African cohort predominantly infected with HIV

Abstract

Hepatitis B virus (HBV) is a serious global health problem, and HBV genotype is an important determinant of disease progression and treatment outcome. The aim of this study was to assess variations of the precore/core (preC/C) region in HBV genotype A. Sequencing of the preC/C and surface (S) genes of HBV was performed on plasma samples from 20 HBV/HIV co-infected and 5 HBV mono-infected individuals. All preC/C study sequences clustered with subgenotype A1, except for two which clustered with subgenotype D4 reference strains. The nucleotide and amino acid variability was far higher in the preC/C region than in the S region. Mutations associated with reduction or failure of HBV e-antigen (HBeAg) production were observed, with a preC start codon mutation being common (24%). Other mutations (e.g., P5H/L and I97L) associated with severe liver disease were also noticed, some of which were located in the major histocompatibility restricted sites. PreC/C intergenotype nucleotide divergence was >7%, while subgenotypes differed by 2.5-7%. Several study sequences were highly divergent from other African subgenotype A1 strains. This study showed that HBeAg-negative chronic hepatitis B is underestimated in subgenotype A1, and also highlighted the variant South African A1 strains. The major advantage of preC/C sequencing is that it informs patient management as HBeAg-negative chronic hepatitis B responds poorly to conventional interferon-α therapy, and some guidelines treat HBeAg-negative chronic hepatitis B differently from HBeAg-positive chronic hepatitis B. These data suggest that subgenotype A1 may be more involved in severe HBV-related diseases.

Keywords: HBeAg-negative chronic hepatitis B; amino acids; genotyping; mutations; nucleotides.

Fig. 1

Phylogenetic analysis of: (A) the preC/C gene and (B) S gene sequences using a Bayesian inference approach. Relevant posterior probabilities >0.9 are shown. CAR, Central African Republic; USA, United States of America. Study sequences are highlighted with a square shaped bullet. S gene dataset had three more reference strains, which were only S gene sequences, hence they were not used in the preC/C data set.

Fig. 1

Phylogenetic analysis of: (A) the preC/C gene and (B) S gene sequences using a Bayesian inference approach. Relevant posterior probabilities >0.9 are shown. CAR, Central African Republic; USA, United States of America. Study sequences are highlighted with a square shaped bullet. S gene dataset had three more reference strains, which were only S gene sequences, hence they were not used in the preC/C data set.

Fig. 2

Frequency of mutations in the major histocompatibility complex class I and II (MHC-I and -II) restricted sites of the Core gene. aa, amino acids, ^*study sequences ended at 146th amino acid (39 aa short from the end of core gene).

Fig. 3

Histogram data showing the distribution of pairwise genetic distances among study and reference sequences. The arrows demarcate different ranges for the intra-subgenotype (0.0 to <0.25), inter-subgenotype (0.25 to <0.07), and intergenotype isolates (≥0.07). The genetic distances for the atypical study sequences (N199, 3274, N60, 3269, 3319, N005, and 3658) were plotted separately (in red), and can be seen to fall in the inter-subgenotype section.