Journal of Molecular Evolution

, Volume 65, Issue 2, pp 197–205 | Cite as

Bayesian Estimates of the Evolutionary Rate and Age of Hepatitis B Virus

  • Yang Zhou
  • Edward C. Holmes


Accurately estimating the evolutionary rate and age of hepatitis B virus (HBV) has proven to be one of the most difficult problems in studies of viral evolution. To help resolve these issues we employed a recently developed Bayesian coalescent approach to globally sampled human and avian hepadnavirus genome sequences, accounting for lineage-specific rate variation, the presence of overlapping reading frames, and the potential impact of recombination. Our analysis revealed an unexpectedly high rate of evolutionary change—up to 10−4 nucleotide substitutions (subs) per site per year and always more than ~10−6 subs/site/year. These rates suggested a time to the most recent common ancestor (tMRCA) of the sampled isolates of consistently less than ~1500 years ago for human HBV and less than 6000 years ago for the avian hepadnaviruses. Notably, the evolutionary rate of nonoverlapping regions of the viral genome was ~2-fold greater than that of overlapping genome regions, reflecting the complex patterns of selective constraint inherent in the former. We also reveal that most recombination events in both human and avian HBV tend to fall in a specific region of the viral genome, which contains all four viral open reading frames and which may therefore represent a “hot spot” for recombination. However, while recombination affects estimates of both evolutionary rate and tMRCA, in no case was this sufficient to challenge the hypothesis that the dominant mode of HBV evolution is by recent cross-species transmission. We conclude that HBV exhibits rapid evolutionary dynamics, typical of other viruses dependent on reverse transcriptase-mediated replication.


Hepatitis B virus Relaxed molecular clock Phylogeny recombination Most recent common ancestor 



We thank Dr. K. Abe, Dr. R. Chakravarty, Dr. Y. Tanaka, Dr. H. Okamoto, Dr. F. Pujol, Dr, Y. Muraki, Dr. K. Fujiwara, Dr. Y. Wen, Dr. P. Karayiannis, Dr. J. Newbold, Dr. W. Hans, Dr. J. Giambrone, and Dr. M. Kew for kindly providing additional information concerning the sequences they generated.

Supplementary material

239_2007_54_Supp.pdf (750 kb)
Supplementary material


  1. Bollyky PL, Holmes EC (1999) Reconstructing the complex evolutionary history of hepatitis B virus. J Mol Evol 49:130–141PubMedCrossRefGoogle Scholar
  2. Bollyky PL, Rambaut A, Harvey PH, Holmes EC (1996) Recombination between sequences of hepatitis B Virus from different genotypes. J Mol Evol 42:97–192PubMedCrossRefGoogle Scholar
  3. Bowyer SM, Sim JGM (2000) Relationships within and between genotypes of hepatitis B virus at points across the genome: footprints of recombination in certain isolates. J Gen Virol 81:379–392PubMedGoogle Scholar
  4. Cui C, Shi J, Hui L, Xi H, Zhuoma, Quni, Tsedan, Hu G (2002) The dominant hepatitis B virus genotype identified in Tibet is a C/D hybrid. J Gen Virol 83:2773–2777PubMedGoogle Scholar
  5. Drake JW, Charlesworth B, Charlesworth D, Crow JF (1998) Rates of spontaneous mutation. Genetics 148:1667–1686PubMedGoogle Scholar
  6. Drummond AJ, Rambaut A (2003) BEAST v1.0. Available at:
  7. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307–1320PubMedGoogle Scholar
  8. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185–1192PubMedCrossRefGoogle Scholar
  9. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 88:699–710Google Scholar
  10. Fares MA, Holmes EC (2002) A revised evolutionary history of hepatitis B virus (HBV). J Mol Evol 54:807–814PubMedCrossRefGoogle Scholar
  11. Hanada K, Suzuki Y, Gojobori T (2004) A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol 21:1074–1080PubMedCrossRefGoogle Scholar
  12. Hannoun C, Horal P, Lindh M (2000) Long-term mutation rates in the hepatitis B virus genome. J Gen Virol 81:75–83PubMedGoogle Scholar
  13. Jenkins GM, Rambaut A, Pybus OG, Holmes EC (2002) Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54:156–165PubMedCrossRefGoogle Scholar
  14. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  15. Kurbanov F, Tanaka Y, Fujiwara K, Sugauchi F, Mbanya D, Zekeng L, Ndembi N, Ngansop C, Kaptue L, Miura T, Ido E, Hayami M, Ichimura H, Mizokami M (2005) A new subtype (subgenotype) Ac (A3) of hepatitis B virus and recombination between genotypes A and E in Cameroon. J Gen Virol 86:2047–2056PubMedCrossRefGoogle Scholar
  16. Luo K, Liu Z, He H, Peng J, Liang W, Dai W, Hou J (2004) The putative recombination of hepatitis B virus genotype B with pre-C/C region of genotype C. Virus Genes 29:31–41PubMedCrossRefGoogle Scholar
  17. Martin DP, Williamson C, Posada D (2005a) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262PubMedCrossRefGoogle Scholar
  18. Martin DP, van der Walt E, Posada D, Rybicki EP (2005b) The evolutionary value of recombination is constrained by genome modularity. PloS Genet 51:475–479Google Scholar
  19. Mizokami M, Orito E, Ohba K, Ikeo K, Lau JYN, Gojobori T (1997) Constrained evolution with respect to gene overlap of hepatitis B virus. J Mol Evol 44:83–90CrossRefGoogle Scholar
  20. Okamoto H, Imai M, Kametani M, Nakamura T, Mayumi M (1987) Genomic heterogeneity of hepatitis B virus in a 54-year-old woman who contracted the infection through materno-fetal transmission. Japan J Exp Med 57:231–236Google Scholar
  21. Olinger CM, Venard V, Njayou M, Oyefolu AO, Maiga I, Kemp AJ, Omilabu SA, le Faou A, Muller CP (2006) Phylogenetic analysis of the precore/core gene of hepatitis B virus genotypes E and A in West Africa: new subtypes, mixed infections and recombinations. J Gen Virol 87:1163–1173PubMedCrossRefGoogle Scholar
  22. Orito E, Mizokami M, Ina Y, Moriyama EN, Kameshima N, Yamamoto M, Gojobori T (1989) Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proc Natl Acad Sci USA 86:7059–7062PubMedCrossRefGoogle Scholar
  23. Osiowy C, Giles E, Tanaka Y, Mizokami Y, Minuk GY (2006) Molecular evolution of hepatitis B virus over 25 years. J Virol 80:10307–10314PubMedCrossRefGoogle Scholar
  24. Simmonds P (2001) Reconstructing the origins of human hepatitis viruses. Phil Trans R Soc Lond B 356:1013–1026CrossRefGoogle Scholar
  25. Simmonds P, Midgley S (2005) Recombination in the genesis and evolution of hepatitis B virus genotypes. J Virol 79:15467–15476PubMedCrossRefGoogle Scholar
  26. Suwannakarn K, Tangkijvanich P, Theamboonlers A, Abe K, Poovorawan Y (2005) A novel recombinant of Hepatitis B virus genotypes G and C isolated from a Thai patient with hepatocellular carcinoma. J Gen Virol 86:3027–3330PubMedCrossRefGoogle Scholar
  27. Swofford D (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4 ed. Sinauer Associates, Sunderland, MAGoogle Scholar
  28. Starkman S, MacDonald DM, Lewis JCM, Holmes EC, Simmonds P (2003) Geographic and species association of hepatitis B virus genotypes in non-human primates. Virology 314:381–393PubMedCrossRefGoogle Scholar
  29. Wang Z, Liu Z, Zeng G, Wen S, Qi Y, Ma S, Naoumov NV, Hou J (2005) A new intertype recombinant between genotypes C and D of hepatitis B virus identified in China. J Gen Virol 86:985–990PubMedCrossRefGoogle Scholar
  30. World Health Organization (2000) Hepatitis B: World Health Organization fact sheet 204. Available at:
  31. Yang J, Xing K, Deng R, Wang J, Wang X (2006) Identification of Hepatitis B virus putative intergenotype recombinants by using fragment typing. J Gen Virol 87:2203–2215PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Center for Infectious Disease Dynamics, Department of BiologyThe Pennsylvania State University, Mueller LaboratoryUSA
  2. 2.Fogarty International CenterNational Institutes of HealthBethesdaUSA

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