Molecular Evolution and Phylodynamics of Acute Hepatitis B Virus in Japan

Abstract

Hepatitis B virus (HBV) is prevalent worldwide and causes liver diseases, including acute and chronic hepatitis. Ten HBV genotypes (A-J) with distinct geographic distributions have been reported. Cases of acute HBV infection with genotype A have increased in Japan nationwide since the 1990s, mainly through sexual transmission. To investigate the molecular evolution and phylodynamics of HBV genotypes, we collected acute HBV isolates acquired in Japan from 1992-2002. Full genomes were obtained for comprehensive phylogenetic and phylodynamic analysis, with other Japanese HBV sequences from GenBank that were isolated during 1991-2010. HBV genotypes were classified using the maximum-likelihood and Bayesian methods. The GMRF Bayesian Skyride was used to estimate the evolution and population dynamics of HBV. Four HBV genotypes (A, B, C, and H) were identified, of which C was the major genotype. The phylodynamic results indicated an exponential growth between the 1960s and early 1990s; this was followed by a population bottleneck after 1995, possibly linked with successful implementation of a nationwide vaccination program. However, HBV/A increased from 1990 to 2003-2004, and then started to decrease. The prevalence of genotype A has increased over the past 10 years. Phylodynamic inference clearly demonstrates a steady population growth compatible with an ongoing subepidemic; this might be due to the loss of immunity to HBV in adolescents and people being born before the vaccination program. This is the first phylodynamic study of HBV infection in Japan and will facilitate understanding the molecular epidemiology and long-term evolutionary dynamics of this virus in Japan.

Fig 1. Phylogenetic tree of HBV S gene reconstructed by Bayesian inference.

The posterior probabilities higher than 0.95 and the star (* = bootstrap value greater than 75) on the branches indicate a significant cluster. Red triangles present acute hepatitis (AH) samples obtained from Japan (n = 57) were divided into genotype A, B, C and H.

Fig 2. Phylogenetic tree of HBV C gene reconstructed by Bayesian inference.

The posterior probabilities higher than 0.95 and the star (* = bootstrap value great than 75) on the branches indicate a significant cluster. Red triangles present samples obtained from Japan (n = 48) were divided into genotype A, B, C and H.

Fig 3. Phylodynamic analysis of HBV in Japan.

Full genome of acute hepatitis B sequences and other Japanese HBV sequences from GenBank were included for GMRF Skyride analysis. The solid black line indicates the mean effective viral population size, as well, the genetic diversity. The genetic diversity of HBV in Japan has subsided since 1995. This change indicated that the virus was been through a bottleneck and agreed by both Upper and Lower HPD 95% curve.

Fig 4. Phylodynamic analysis of genotype A in Japan.

Full genomes of acute HBV genotype A samples and other Japanese HBV genotype A sequences retrieved from GenBank were used to run Skyride analysis. The Upper HPD 95% shows stable population maintaining over time while the Lower HPD 95% of effective number of viral population suggests exponential growing from early 1990 and a quick decline after 2003. However, the mean of genetic diversity (the solid black line) revealed that HBV/A population is substantially increasing from 1990 to 2003 and decreased since 2005.