Genotype, serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus

Abstract

Hepatitis B virus (HBV) genotypes have distinct geographical distribution. HBV sequences among hepatitis B carriers in Malawi have not been evaluated thus far. HBsAg serotype and genotype of HBV was determined in 20 serum samples from Malawian chronic HBV carriers, and two complete genomes and 13 entire pre-S2/S genes were sequenced directly. Genotype A HBV isolates were found in all of the samples, and serotype with adw2 and ayw2 were detected in three and 17 samples, respectively. In phylogenetic analyses, two complete genomes were classified into a subgroup A' that was described previously in South African isolates of the virus, and were separated from HBV isolates in Western countries with nucleotide differences ranging from 4.1-6.2%. The separation of subgroup A' was also evident in the tree topology of the entire pre-S1/S2, X and precore/core region, but not evident in the small-S region. The nucleotide divergences in subgroup A' were higher than those among genotype A without subgroup A' in the complete genomes as well as each of four open reading frames. All of the 13 pre-S2/S sequences were classified into the subgroup A', and clustered with known HBV isolates with ayw2 in carriers from South Africa and Zimbabwe. Three amino acids in the pre-S2/S gene were characteristic of subgroup A' with ayw2. In conclusion, unique HBV isolates of subgroup A' with ayw2 are prevalent in Malawi, and subgroup A' with a relatively higher nucleotide diversity may be a HBV isolate characteristic of the indigenous population of some African countries.

Evaluation of the INNO-LiPA HBV Genotyping Assay for Determination of Hepatitis B Virus Genotype

“…The pre-S region has also been used for genotyping purposes (15), and it occasionally distinguishes genotypes not able to be typed by analysis of the S gene alone (1,15,29). Even so, our results demonstrated a high degree of correlation between the genotypes determined by genotyping of the pre-S region and genotyping of the S region, as has been observed previously (15).…”

Novel Hepatitis B Virus Genotype A Subtyping Assay That Distinguishes Subtype Aa from Ae and Its Application in Epidemiological Studies

“…In previous studies, when HBV isolates showing intergenotypic recombination were excluded, subtype AЈ (HBV/Aa) was clearly distinguished by phylogenetic analyses from the remaining genotype A (HBV/Ae) in each of the open reading frames except for the small S region (29,30). Examining all available full HBV sequences from the databases, nucleotide sequences that could distinguish HBV/Aa from HBV/Ae were found in the X/precore/core region.…”

“…A large number of HBV isolates from South Africa were found to cluster with this subtype AЈ by phylogenetic analyses of both the pre-S2/S region (5) and the complete genome (13,16). This subtype has also been found in HBV isolates from Malawi (29). In African countries, genotype A isolates, most of which are subtype AЈ, seem to be associated with low levels of HBV DNA in serum and a low prevalence of hepatitis B e antigen (HBeAg) in serum (14,15).…”

Low Genetic Diversity despite Hyperendemicity of Hepatitis B Virus Genotype E throughout West Africa

“…Strains DRC14574 and DRC020033 from Kinshasa belonged to HBV/E, whereas Lux92-25059DRC, isolated in Luxembourg in 1992 from an individual born in the DRC, was most closely related to a Malawian HBV/A strain [23]. Strain DRC0300441, isolated from a 48-year-old woman, also belonged to HBV/A and is most closely related to the Cameroon HBV/A strains.…”