Origin of HBV and its arrival in the Americas - The importance of natural selection on time estimates

Antiviral Therapy

Volumn 18, Issue 3 PARTB, 2013, Pages 505-512

  Godoy, Bibiane A ^a,b   Alvarado Mora, Mónica V ^c   Gomes Gouvêa, Michele S ^c   Rebello Pinho, João R ^c   Fagundes, Nelson J R ^a,b  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b National Institute for Populational Medical Genetics   (Brazil)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

ARTICLE; BAYES THEOREM; GENOTYPE; GEOGRAPHIC ORIGIN; HEPATITIS B VIRUS; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS GENOME; WESTERN HEMISPHERE;

CENTRAL AMERICA; DNA, VIRAL; GENETIC VARIATION; GENOME, VIRAL; GENOTYPE; HEPATITIS B; HEPATITIS B VIRUS; HUMANS; MOLECULAR EPIDEMIOLOGY; MUTATION; MUTATION RATE; NORTH AMERICA; SELECTION, GENETIC; SOUTH AMERICA;

EID: 84879675106     PISSN: 13596535     EISSN: 20402058     Source Type: Journal    
DOI: 10.3851/IMP2600     Document Type: Article

References (36)

1. Lai CL, Ratziu V, Yuen M F, Poynard T. Viral hepatitis B. Lancet 2003; 362:2089-2094.
2. Yu H, Yuan Q, Ge SX, et al. Molecular and phylogenetic analyses suggest an additional hepatitis B virus genotype 'I'. PLoS ONE 2010; 5:e9297.
3. Schaefer S. Hepatitis B virus taxonomy and hepatitis B virus genotypes. World J Gastroenterol 2007; 13:14-21.
4. Devesa M, Pujol FH. Hepatitis B virus genetic diversity in Latin America. Virus Res 2007; 127:177-184.
5. Roman S, Tanaka Y, Khan A, et al. Occult hepatitis B in the genotype H-infected Nahuas and Huichol native Mexican population. J Med Virol 2010; 82:1527-1536.
6. Alvarado-Mora MV, Romano CM, Gomes-Gouvea MS, et al. Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F. Infect Genet Evol 2011; 11:103-108.
7. Motta-Castro AR, Martins RM, Araujo NM, et al. Molecular epidemiology of hepatitis B virus in an isolated Afro-Brazilian community. Arch Virol 2008; 153:2197-2205.
8. Santos AO, Alvarado-Mora MV, Botelho L, et al. Characterization of hepatitis B virus (HBV) genotypes in patients from Rondonia, Brazil. Virol J 2010; 7:315.
9. Alvarado-Mora MV, Romano CM, Gomes-Gouvea MS, Gutierrez MF, Carrilho FJ, Pinho JRR. Molecular epidemiology and genetic diversity of hepatitis B virus genotype E in an isolated Afro-Colombian community. J Gen Virol 2010; 91:501-508.
10. Piñeiro y Leone FG, Pezzano SC, Torres C, et al. Hepatitis B virus genetic diversity in Argentina: dissimilar genotype distribution in two different geographical regions; description of hepatitis B surface antigen variants. J Clin Virol 2008; 42:381-388.
11. Torres C, Piñeiro y Leone FG, Pezzano SC, Mbayed VA, Campos RH. New perspectives on the evolutionary history of hepatitis B virus genotype F. Mol Phylogenet Evol 2011; 59:114-122.
12. Zhou Y, Holmes EC. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J Mol Evol 2007; 65:197-205.
13. Hannoun C, Horal P, Lindh M. Long-term mutation rates in the hepatitis B virus genome. J Gen Virol 2000; 81:75-83.
14. Ho SYW, Larson G. Molecular clocks: when times are a-changin'. Trends Genet 2006; 22:79-83.
15. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 2005; 22:1561-1568.
16. Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE 2008; 3:e1615.
17. Ho SYW, Lanfear R, Bromham L, et al. Time-dependent rates of molecular evolution. Mol Ecol 2011; 20:3087-3101.
18. Crandall ED, Sbrocco EJ, DeBoer TS, et al. Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the last glacial maximum. Mol Biol Evol 2012; 29:707-719.
19. Kivisild T, Shen P, Wall D, et al. The role of selection in the evolution of human mitochondrial genomes. Genetics 2006; 172:373-387.
20. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214.
21. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006; 4:e88.
22. *and other methods). Version 4.0b10. Sunderland, MA: Sinauer Associates 2003.
23. Posada D, Crandall KA. Modeltest: testing the model of DNA substitution. Bioinformatics 1998; 14:817-818.
24. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009; 25:1451-1452.
25. Abramson JH, Gahlinger PM. Computer programs for epidemiologists: PEPI v 4.0. Salt Lake City, UT: Sagebrush Press 2001.
26. Bar-Gal GK, Kim MJ, Klein A, et al. Tracing hepatitis B virus to the 16th century in a Korean mummy. Hepatology 2012; 56:1671-1680.
27. Ott JJ, Stevens GA, Groeger J, Wiersma ST. Global epidemiology of hepatitis B virus infection: new estimates of age-specific HBsAg seroprevalence and endemicity. Vaccine 2012; 30:2212-2219.
28. Lim SG, Cheng Y, Guindon S, et al. Viral quasispecies during hepatitis B e antigen seroconversion. Gastroenterology 2007; 133:951-958.
29. Harrison A, Lemey P, Hurles M, et al. Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses 2011; 3:83-101.
30. Fagundes NJR, Kanitz R, Eckert R, et al. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Genet 2008; 82:583-592.
31. Tamm E, Kivisild T, Reidla M, et al. Beringian standstill and spread of Native American founders. PLoS ONE 2007; 2:e829.
32. Dillehay TD. Monte Verde: a late Pleistocene settlement in Chile. The archaeological context and interpretation. Vol. 2. Washington, DC: Smithsonian Institution Press 1997.
33. Ray N, Wegmann D, Fagundes NJR, Wang S, Ruiz-Linares A, Excoffier L. A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia. Mol Biol Evol 2010; 27:337-345.
34. Arauz-Ruiz P, Norder H, Robertson BH, Magnius LO. Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America. J Gen Virol 2002; 83:2059-2073.
35. Venegas M, Alvarado-Mora MV, Villanueva RA, et al. Phylogenetic analysis of hepatitis B virus genotype F complete genome sequences from Chilean patients with chronic infection. J Med Virol 2011; 83:1530-1536.
36. Arauz-Ruiz P, Norder H, Visona KA, Magnius LO. Genotype F prevails in HBV infected patients of hispanic origin in Central America and may carry the precore stop mutant. J Med Virol 1997; 51:305-312.