The strong geographic structure shown by the global pattern of HBV lineages suggests an ancient origin for this virus; however, estimates based on the molecular clock suggest a very recent origin for the Native American genotypes F and H. In this study, we contribute to this debate by estimating the divergence times of genotypes F and H and by discussing how evolutionary rates estimated from recent samples may underestimate the divergence time of more ancient nodes in HBV phylogenies.
Methods
A total of 108 complete HBV genotype F and H genomes were compared to 44 reference genomes from other genotypes. Time estimates were based on a Bayes-ian method with evolutionary rates taken from the literature. To assess the pattern of substitutions in recent versus old branches we mapped the phylogenetic distribution of all mutations occurring in genotypes F and H using a maximum likelihood approach and compared the number of synonymous and non-synonymous mutations in young and old branches of HBV genotype F and H phylogeny using a c2 test.
Results
Estimated divergence times between genotypes F and H depend heavily on the evolutionary rate. While fast rates suggest a recent separation of these genotypes (approximately 800 years ago), slow rates suggest an earlier divergence (up to approximately 13,000 years ago). There is a clear excess of non-synonymous substitutions in the most recent branches of HBV phylogeny (P=4.87x10-15), most likely suggesting the action of purifying selection.
Conclusions
These results suggest that rates estimated based on recent samples will overestimate the evolutionary rate and underestimate the coalescence times for ancient nodes in HBV phylogeny.
References
1.
LaiC.L., RatziuV., YuenM.F., PoynardT.Viral hepatitis B. Lancet2003; 362: 2089–2094.
2.
YuH., YuanQ., GeS.X.Molecular and phylogenetic analyses suggest an additional hepatitis B virus genotype ‘I'. PLoS ONE2010; 5: e9297.
3.
SchaeferS.Hepatitis B virus taxonomy and hepatitis B virus genotypes. World J Gastroenterol2007; 13: 14–21.
4.
DevesaM., PujolF.H.Hepatitis B virus genetic diversity in Latin America. Virus Res2007; 127: 177–184.
5.
RomanS., TanakaY., KhanA.Occult hepatitis B in the genotype H-infected Nahuas and Huichol native Mexican population. J Med Virol2010; 82: 1527–1536.
6.
Alvarado-MoraM.V., RomanoC.M., Gomes-GouveaM.S.Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F. Infect Genet Evol2011; 11: 103–108.
7.
Motta-CastroA.R., MartinsR.M., AraujoN.M.Molecular epidemiology of hepatitis B virus in an isolated Afro-Brazilian community. Arch Virol2008; 153: 2197–2205.
8.
SantosA.O., Alvarado-MoraM.V., BotelhoL.Characterization of hepatitis B virus (HBV) genotypes in patients from Rondonia, Brazil. Virol J2010; 7: 315.
9.
Alvarado-MoraM.V., RomanoC.M., Gomes-GouveaM.S., GutierrezM.F., CarrilhoF.J., PinhoJ.R.R.Molecular epidemiology and genetic diversity of hepatitis B virus genotype E in an isolated Afro-Colombian community. J Gen Virol2010; 91: 501–508.
10.
Piñeiro y LeoneF.G., PezzanoS.C., TorresC.Hepatitis B virus genetic diversity in Argentina: dissimilar genotype distribution in two different geographical regions; description of hepatitis B surface antigen variants. J Clin Virol2008; 42: 381–388.
11.
TorresC., Piñeiro y LeoneF.G., PezzanoS.C., MbayedV.A., CamposR.H.New perspectives on the evolutionary history of hepatitis B virus genotype F. Mol Phylogenet Evol2011; 59: 114–122.
12.
ZhouY., HolmesE.C.Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J Mol Evol2007; 65: 197–205.
13.
HannounC., HoralP., LindhM.Long-term mutation rates in the hepatitis B virus genome. J Gen Virol2000; 81: 75–83.
14.
HoS.Y.W., LarsonG.Molecular clocks: when times are a-changin'. Trends Genet2006; 22: 79–83.
15.
HoS.Y.W., PhillipsM.J., CooperA., DrummondA.J.Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol2005; 22: 1561–1568.
16.
HoS.Y.W., SaarmaU., BarnettR., HaileJ., ShapiroB.The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE2008; 3: e1615.
CrandallE.D., SbroccoE.J., DeBoerT.S.Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the last glacial maximum. Mol Biol Evol2012; 29: 707–719.
19.
KivisildT., ShenP., WallD.The role of selection in the evolution of human mitochondrial genomes. Genetics2006; 172: 373–387.
DrummondA.J., HoS.Y.W., PhillipsM.J., RambautA.Relaxed phylogenetics and dating with confidence. PLoS Biol2006; 4: e88.
22.
SwoffordD.L.PAUP*: Phylogenetic Analysis using Parsimony (*and other methods). Version 4.0b10. Sunderland, MA: Sinauer Associates2003.
23.
PosadaD., CrandallK.A.Modeltest: testing the model of DNA substitution. Bioinformatics1998; 14: 817–818.
24.
LibradoP., RozasJ.DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics2009; 25: 1451–1452.
25.
AbramsonJ.H., GahlingerP.M.Computer programs for epidemiologists: PEPI v 4.0. Salt Lake City, UT: Sagebrush Press2001.
26.
Bar-GalG.K., KimM.J., KleinA.Tracing hepatitis B virus to the 16th century in a Korean mummy. Hepatology2012; 56: 1671–1680.
27.
OttJ.J., StevensG.A., GroegerJ., WiersmaS.T.Global epidemiology of hepatitis B virus infection: new estimates of age-specific HBsAg seroprevalence and endemicity. Vaccine2012; 30: 2212–2219.
28.
LimS.G., ChengY., GuindonS.Viral quasi-species during hepatitis B e antigen seroconversion. Gastroenterology2007; 133: 951–958.
29.
HarrisonA., LemeyP., HurlesM.Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses2011; 3: 83–101.
30.
FagundesN.J.R., KanitzR., EckertR.Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Genet2008; 82: 583–592.
31.
TammE., KivisildT., ReidlaM.Beringian standstill and spread of Native American founders. PLoS ONE2007; 2: e829.
32.
DillehayT.D.Monte Verde: a late Pleistocene settlement in Chile. The archaeological context and interpretation. Vol. 2. Washington, DC: Smithsonian Institution Press1997.
33.
RayN., WegmannD., FagundesN.J.R., WangS., Ruiz-LinaresA., ExcoffierL.A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia. Mol Biol Evol2010; 27: 337–345.
34.
Arauz-RuizP., NorderH., RobertsonB.H., MagniusL.O.Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America. J Gen Virol2002; 83: 2059–2073.
35.
VenegasM., Alvarado-MoraM.V., VillanuevaR.A.Phylogenetic analysis of hepatitis B virus genotype F complete genome sequences from Chilean patients with chronic infection. J Med Virol2011; 83: 1530–1536.
36.
Arauz-RuizP., NorderH., VisonaK.A., MagniusL.O.Genotype F prevails in HBV infected patients of hispanic origin in Central America and may carry the precore stop mutant. J Med Virol1997; 51: 305–312.
