New complex recombinant genotype of hepatitis B virus identified in Vietnam

Abstract

A novel variant of hepatitis B virus was identified in Vietnam. This strain (HBV-VH24) had a novel intergenotypic recombination between genotypes A, C, and G. VH24 showed high similarity (98.3 to 98.9%) to the "aberrant strains" among Vietnamese isolates reported by Hannoun et al. (C. Hannoun et al., J. Gen. Virol. 81:2267-2272, 2000) and also had similar breakpoints of recombination. Phylogenetic analysis of the complete genome of these strains formed a separate clade. Furthermore, their pre-S/S gene-encoded seven unique conserved amino acid residues were not present in other genotypes. These findings support the designation of the new genotype I.

FIG. 1.

Phylogenetic neighbor-joining tree constructed using full-length genome (A), pre-S gene (B), and S gene (C) of HBV, including VH24 (AB231908 in the present study) and three aberrant strains from the database (AF241407, AF241408, and AF241409). Bootstrap values were indicated at each tree roots (percentage of 1,000 bootstrap replicates that support the branch). The sequence AY090454 of genotype H was used as an outgroup. Only bootstrap values of >60% are indicated. The horizontal bar provides a genetic distance.

FIG. 1.

Phylogenetic neighbor-joining tree constructed using full-length genome (A), pre-S gene (B), and S gene (C) of HBV, including VH24 (AB231908 in the present study) and three aberrant strains from the database (AF241407, AF241408, and AF241409). Bootstrap values were indicated at each tree roots (percentage of 1,000 bootstrap replicates that support the branch). The sequence AY090454 of genotype H was used as an outgroup. Only bootstrap values of >60% are indicated. The horizontal bar provides a genetic distance.

FIG. 1.

Phylogenetic neighbor-joining tree constructed using full-length genome (A), pre-S gene (B), and S gene (C) of HBV, including VH24 (AB231908 in the present study) and three aberrant strains from the database (AF241407, AF241408, and AF241409). Bootstrap values were indicated at each tree roots (percentage of 1,000 bootstrap replicates that support the branch). The sequence AY090454 of genotype H was used as an outgroup. Only bootstrap values of >60% are indicated. The horizontal bar provides a genetic distance.

FIG. 2.

Bootscan analysis demonstrating the complex recombination between genotypes A, C, and G in isolate VH24 (A) and reported aberrant Vietnamese isolate AF241407 (B). These two strains were subjected to bootscan analysis over the complete genome using the Simplot program with a 200-bp window size, 20-bp step size, and 100 bootstrap replicates, using gap-stripped alignments and neighbor-joining analysis. Strains were compared to three representative HBV genotypes: A (accession no. AB126580), C (accession no. AB049609), and G (accession no. AB056513). The dotted vertical lines showed the common estimated breakpoints of recombination in both analyzed strains.

FIG. 3.

Multi-alignment of deduced amino acid sequence the large S gene (amino acids 1 to 400) of genotypes A (subgenotypes A1 and A2), C (subgenotype C1 in Vietnam), and G and new variant strains. The VH24 and other aberrant strains showed identical deduced amino acids in the large S gene. Boldface characters show specific amino acid changes found in this new variant group compared to genotypes A, C, and G.