Molecular Characterization of Near Full-Length Genomes of Hepatitis B Virus Isolated from Predominantly HIV Infected Individuals in Botswana

Abstract

The World Health Organization plans to eliminate hepatitis B and C Infections by 2030. Therefore, there is a need to study and understand hepatitis B virus (HBV) epidemiology and viral evolution further, including evaluating occult (HBsAg-negative) HBV infection (OBI), given that such infections are frequently undiagnosed and rarely treated. We aimed to molecularly characterize HBV genomes from 108 individuals co-infected with human immunodeficiency virus (HIV) and chronic hepatitis B (CHB) or OBI identified from previous HIV studies conducted in Botswana from 2009 to 2012. Full-length (3.2 kb) and nearly full-length (~3 kb) genomes were amplified by nested polymerase chain reaction (PCR). Sequences from OBI participants were compared to sequences from CHB participants and GenBank references to identify OBI-unique mutations. HBV genomes from 50 (25 CHB and 25 OBI) individuals were successfully genotyped. Among OBI participants, subgenotype A1 was identified in 12 (48%), D3 in 12 (48%), and E in 1 (4%). A similar genotype distribution was observed in CHB participants. Whole HBV genome sequences from Botswana, representing OBI and CHB, were compared for the first time. There were 43 OBI-unique mutations, of which 26 were novel. Future studies using larger sample sizes and functional analysis of OBI-unique mutations are warranted.

Keywords: Africa; Botswana; HBV; chronic hepatitis B; mutations; occult hepatitis B.

Figure 1

A phylogenetic tree of the whole surface region (nucleotide (nt) 2854–835 from EcoRI site) of subgenotype A1 hepatitis B virus (HBV) sequences generated by Bayesian Evolutionary Analysis by Sampling Trees (BEAST). Strains from Botswana sequenced in the present study are shown in blue, while reference sequences are shown in black. Reference strains are designated by their accession number and country of origin, whereas Botswana sequences are designated by MA followed by a number and either CHB (for chronic HBV strains) or OBI (for occult HBV strains).

Figure 2

A phylogenetic tree of the whole surface region (nt 2854–835 from EcoRI site) of HBV subgenotype D3 generated by BEAST. Botswana sequences are shown in blue, whereas reference sequences are in black. Reference strains are designated by their accession number and country of origin, whereas Botswana sequences are designated by MA followed by a number and either CHB or OBI.