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. 2025 Jan 17;12(1):e99010048.
doi: 10.14440/jbm.2025.0084. eCollection 2025.

Phylodynamics of hepatitis B virus genotype B in East Asia: A population genomics analysis

Serena Y C Lin  1 , Patrick C Y Woo  2   3
Affiliations

Phylodynamics of hepatitis B virus genotype B in East Asia: A population genomics analysis

Serena Y C Lin et al. J Biol Methods. .

Abstract

Background: Hepatitis B virus (HBV) genotype B (HBV/B) is the predominant strain in Taiwan and several East Asian countries.

Objective: The aim of this study is to use comprehensive phylogenetic analysis tools to monitor the long-term molecular evolution dynamic of HBV genotype B population in East Asia.

Methods: In this study, full genome sequences of HBV with temporal information were extracted from GenBank and analyzed using the Bayesian Markov chain Monte Carlo method to identify best-fitting coalescent models.

Results: Bayesian Skygrid analysis revealed a viral effective population (phylodynamic) bottleneck for HBV/B in 2003, a pattern similar to the previously described HBV genotype C (HBV/C). Despite these similarities, the viral dynamics for HBV/B and HBV/C diverged after 2005. HBV/C exhibited a marked decrease in genetic diversity across East Asia, whereas HBV/B maintained stable genetic diversity after 2005. Phylogeographic analysis using Neighbor-Joining and Bayesian maximum clade credibility trees indicated that Taiwan was likely the geographic origin of the most recent common ancestor of HBV/B in East Asia. An early clade spread to Japan and subsequently to the West Coast of the United States of America. Another clade dispersed to China, spread widely across the region, and was reintroduced to Taiwan multiple times. In contrast, HBV/C likely originated in China and spread to Japan, Korea, and Taiwan over several decades.

Conclusion: This study highlights the similarities and differences between the viral dynamics and geographical evolutionary pathways between HBV/B and HBV/C.

Keywords: Bottleneck; East Asia; HBV genotype B; Most recent common ancestor; Phylogeography.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Neighbor-Joining tree reconstructed using HBV/B full genome sequences (n = 331) from East Asian countries. The numbers on the branches represent the bootstrap values. Outgroup sequences (genotype C) are marked light blue for outgroup rooting. Countries are specified according to color. Abbreviations: HBV/B: Hepatitis B virus genotype B.
Figure 2
Figure 2
Maximum Likelihood tree reconstructed using HBV/B full genome sequences (n = 331) from East Asian countries. The numbers on the branches represent likelihood ratio test values (in the format of 0.XX). Outgroup sequences (genotype C) are marked light blue for outgroup-rooting. Countries are specified according to color. Abbreviations: HBV/B: Hepatitis B virus genotype B.
Figure 3
Figure 3
The Bayesian maximum clade credibility tree was reconstructed using HBV/B full genome sequences across East Asian countries (n = 150). Posterior probability (in the format of 0.XX) indicates the statistical results of branching. Countries are specified according to color. Abbreviation: HBV/B: Hepatitis B virus genotype B.
Figure 4
Figure 4
HBV/B and HBV/C phylogeography in East Asian countries visualized using Google Earth. Abbreviations: HBV/B: Hepatitis B virus genotype B; HBV/C: Hepatitis B virus genotype C.
Figure 5
Figure 5
HBV/B and HBV/C genetic diversity in East Asian countries visualized using Skygrid analysis. Abbreviations: HBV/B: Hepatitis B virus genotype B; HBV/C: Hepatitis B virus genotype C.
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