Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation

Viruses

Volumn 3, Issue 2, 2011, Pages 83-101

  Harrison, Abby ^a,b   Lemey, Philippe ^c   Hurles, Matthew ^d   Moyes, Chris ^e   Horn, Susanne ^f   Pryor, Jan ^b   Malani, Joji ^b   Supuri, Mathias ^g   Masta, Andrew ^g   Teriboriki, Burentau ^h   Toatu, Tebuka ^h   Penny, David ⁱ   Rambaut, Andrew ^j,k   Shapiro, Beth ^l  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b Fiji School of Medicine   (United Kingdom)

^c REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e The Hepatitis Foundation of New Zealand   (New Zealand)

^f MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^g School of Medicine and Health Sciences   (United Kingdom)

^h Kiribati Ministry of Health   (United Kingdom)

ⁱ MASSEY UNIVERSITY   (New Zealand)

^j Institute of Evolutionary Biology   (United Kingdom)

^k NATIONAL INSTITUTES OF HEALTH   (United States)

^l PENNSYLVANIA STATE UNIVERSITY   (United States)

more..

Author keywords

Bayesian phylogenetics; Hepatitis b virus; Molecular clock

Indexed keywords

HEPATITIS B ANTIGEN;

ANTIGEN EXPRESSION; ARTICLE; EVOLUTION; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HEPATITIS B VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SEROLOGY; VIRUS EXPRESSION; VIRUS GENOME; VIRUS IMMUNITY; VIRUS MUTATION; VIRUS REPLICATION;

BAYES THEOREM; DATABASES, GENETIC; DNA, VIRAL; EVOLUTION, MOLECULAR; GENOME, VIRAL; HEPATITIS B; HEPATITIS B E ANTIGENS; HEPATITIS B VIRUS; HUMANS; INFECTIOUS DISEASE TRANSMISSION, VERTICAL; MODELS, GENETIC; PACIFIC ISLANDS; PHYLOGENY; TIME FACTORS;

HEPATITIS B VIRUS;

EID: 79952139337     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3020083     Document Type: Article

References (54)

1. Drummond, A.J.; Pybus, O.G.; Rambaut, A.; Forsberg, R.; Rodrigo, A.G. Measurably evolving populations. Trends Ecol. Evol. 2003, 18, 481-488.
2. Drummond, A.; Pybus, O.G.; Rambaut, A. Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. 2003, 54, 331-358.
3. Pybus, O.G.; Rambaut, A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 2009, 10, 540-550.
4. Nakano, T.; Lu, L.; He, Y.; Fu, Y.; Robertson, B.H.; Pybus, O.G. Population genetic history of hepatitis C virus 1b infection in China. J. Gen. Virol. 2006, 87, 73-82.
5. Rodrigo, A.G.; Goode, M.; Forsberg, R.; Ross, H.A.; Drummond, A. Inferring evolutionary rates using serially sampled sequences from several populations. Mol. Biol. Evol. 2003, 20, 2010-2018.
6. Rambaut, A.; Pybus, O.G.; Nelson, M.I.; Viboud, C.; Taubenberger, J.K.; Holmes, E.C. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008, 453, 615-619.
7. Jenkins, G.M.; Rambaut, A.; Pybus, O.G.; Holmes, E.C. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 2002, 54, 156-165.
8. Duffy, S.; Shackleton, L.A.; Holmes, E.C. Rates of evolutionary change in viruses: Patterns and determinants. Nat. Rev. Genet. 2008, 9, 267-276.
9. Shackelton, L.A.; Rambaut, A.; Pybus, O.G.; Holmes, E.C. JC virus evolution and its association with human populations. J. Virol. 2006, 80, 9928-9933.
10. Firth, C.; Kitchen, A.; Shapiro, B.; Suchard, M.A.; Holmes, E.C.; Rambaut, A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol. Biol. Evol. 2010, 27, 2038-2051.
11. Kodama, K.; Ogasawara, N.; Yoshikawa, H.; Murakami, S. Nucleotide sequence of a cloned woodchuck hepatitis virus genome: evolutional relationship between hepadnaviruses. J. Virol. 1985, 56, 978-986.
12. Okamoto, H.; Imai, M.; Kametani, M.; Nakamura, T.; Mayumi, M. Genomic heterogeneity of Hepatitis B virus in a 54 year old woman who contracted the infection through Materno-Fetal transmission. Jpn. J. Exp. Med. 1987, 57, 231-236.
13. Orito, E.; Mizokami, M.; Ina, Y.; Moriyama, E.N.; Kameshima, N.; Yamamoto, M.; Gojobori, T. Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proc. Natl. Acad. Sci. U. S. A. 1989, 86, 7059-7062.
14. Fares, M.A.; Holmes, E.C. A revised evolutionary history of Hepatitis B virus (HBV). J. Mol. Evol. 2002, 54, 807-814.
15. Michitaka, K.; Tanaka, Y.; Horiike, N.; Duong, T.N.; Chen, Y.; Matsuura, K.; Hiasa, Y.; Mizokami, M.; Onj, I.M. Tracing the history of hepatitis B virus genotype D in Western Japan. J. Med. Virol. 2006, 78, 44-52.
16. Osiowy, C.; Giles, E.; Tanaka, Y.; Mizokami, M.; Minuk, G.Y. Molecular Evolution of Hepatitis B virus over 25 years. J. Virol. 2006, 80, 10307-10314.
17. Zhou, Y.; Holmes, E.C. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J. Mol. Evol. 2007, 65, 197-205.
18. Lim, S.G.; Cheng, Y.; Guindon, S.; Seet, B.L.; Lee, L.Y.; Hu, P.; Wasser, S.; Peter, F.J.; Tan, T.; Goode, M.; Rodrigo, A.G. Viral quasi-species evolution during hepatitis Be antigen seroconversion. Gastroenterology 2007, 133, 951-958
19. Simmonds, P. The origin and evolution of hepatitis viruses in humans. J. Gen. Virol. 2001, 82, 693-712.
20. Legrand-Abravanel, F.; Claudinon, J.; Nicot, F.; Dubois, M.; Chapuy-Regaud, S.; Sandres-Saune, K.; Pasquier, C.; Izopet, J. New Natural Intergenotypic (2/5) Recombinant of Hepatitis C Virus. J. Virol. 2007, 81, 4357-4362.
21. Simmonds, P.; Midgley, S. Recombination in the genesis and evolution of hepatitis B virus genotypes. J. Virol. 2005, 79, 15467-15476.
22. Billerbeck, E.; Bottler, T.; Thimme, R. Regulatory T cells in viral hepatitis. World J. Gastroenterol. 2007, 13, 4858-4864.
23. Vanlandschoot, P.; Cao, T.; Leroux-Roels, G. The nucleocapsid of the hepatitis B virus: A remarkable immunogenic structure. Antivir. Res. 2003, 60, 67-74.
24. Beck, J.; Nassal, M. Hepatitis B virus replication. World J. Gastroenterol. 2007, 13, 48-64.
25. Gerner, P.; Lausch, E.; Friedt, M.; Tratzmuller, R.; Spangenberg, C.; Wirth, S. Hepatitis B virus core promoter mutations in children with multiple anti-HBe/HBeAg reactivations result in enhanced promoter activity. J. Med. Virol. 1999, 59, 415-423.
26. Hasegawa, K.; Huang, J.; Rogers, S.A.; Blum, H.E.; Liang, T.J. Enhanced replication of a hepatitis B virus mutant associated with an epidemic of fulminant hepatitis. J. Virol. 1994, 68, 1651-1659.
27. Beasley, R.P.; Trepo, C.; Stevens, C.E.; Szmuness, W. The e antigen and vertical transmission of hepatitis B surface antigen. Am. J. Epidemiol. 1977, 105, 94-98.
28. Blackberg, J.; Kidd-Ljunggren, K. Occult hepatitis B virus after acute self-limited infection persisting for 30 years without sequence variation. J. Hepatol. 2000, 33, 992-997.
29. Bozkaya, H.; Akarca, U.; Ayola, B.; Lok, A.S.F. High degree of conservation in the hepatitis B virus core gene during the immune tolerant phase in perinatally acquired chronic hepatitis B virus infection. J. Hepatol. 1997, 26, 508-516.
30. Günther, S.; Li, B.C.; Miska, S.; Krüger, D.H.; Meisel, H.; Will, H. A novel method for efficient amplification of whole hepatitis B virus genomes permits rapid functional analysis and reveals deletion mutants in immunosuppressed patients. J. Virol. 1995, 69, 5437-5444.
31. Drummond, A.J.; Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7, 214.
32. Drummond, A.J.; Ho, S.Y.; Phillips, M.J.; Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4, e88.
33. Yoshikawa, A.; Gotanda, Y.; Itabashi, M.; Minegishi, K.; Kanemitsu, K.; Nishioka, K. Hepatitis B NAT virus-positive blood donors in the early and late stages of HBV infection: Analyses of the window period and kinetics of HBV DNA. Vox Sang. 2005, 88, 77-86.
34. Zehender, G.; De Maddalena, C.; Giambelli, C.; Milazzo, L.; Schiavini, M.; Bruno, R.; Tanzi, E.; Galli, M. Different evolutionary rates and epidemic growth of hepatitis B virus genotypes A and D. Virology 2008, 380, 84-90.
35. Devesa, M.; Pujol, F.H. Hepatitis B virus genetic diversity in Latin America. Virus Res. 2007, 127, 177-184.
36. Duong, T.N.; Horiike, N.; Michitaka, K.; Yan, C.; Mizokami, M.; Tanaka, Y.; Jyoko, K.; Yamamoto, K.; Miyaoka, H.; Yamashita, Y.; Ohne, N.; Onji, M. Comparison of genotypes C and D of the hepatitis B virus in Japan: a clinical and molecular biological study. J. Med. Virol. 2004, 72, 551-557.
37. Gust, I.D. Epidemiology of hepatitis B infection in the Western Pacific and South East Asia. Gut 1996, 38, S18-S23.
38. Whittle, H.C.; Bradley, A.K.; McLauchlan, K.; Ajdukiewicz, A.B.; Howard, C.R.; Zuckerman, A.J.; McGregor, I.A. Hepatitis B virus infection in two Gambian villages. Lancet 1983, 321, 1203-1206.
39. Seeger, C.; Mason, W.S. Hepatitis B virus biology. Microbiol. Mol. Biol. Rev. 2000, 64, 51-68.
40. Chen, C.H.; Lee, C.M.; Hung, C.H.; Hu, T.H.; Wang, J.H.; Wang, J.C.; Lu, S.N.; Changchien, C.S. Clinical significance and evolution of core promoter and precore mutations in HBeAgpositive patients with HBV genotype B and C: A longitudinal study. Liver Int. 2007, 27, 806-815.
41. Chou, Y.C.; Yu, M.W.; Wu, C.F.; Yang, S.Y.; Lin, C.L.; Liu, C.J.; Shih, W.L.; Chen, P.J.; Liaw, Y.F.; Chen, C.J. Temporal relationship between hepatitis B virus enhancer II/basal core promoter sequence variation and risk of hepatocellular carcinoma. Gut 2008, 57, 91-97.
42. Ho, S.Y.; Heupink, T.H.; Rambaut, A.; Shapiro, B. Bayesian estimation of sequence damage in ancient DNA. Mol. Biol. Evol. 2007, 24, 1416-1422.
43. Kidd-Ljunggren, K.; Oberg, M.; Kidd, A.H. Hepatitis B virus X gene 1751 to 1764 mutations: implications for HBeAg status and disease. J. Gen. Virol. 1997, 78, 1469-1478.
44. Hannoun, C.; Horal, P.; Lindh, M. Long-term mutation rates in the hepatitis B virus genome. J. Gen. Virol. 2000, 81, 75-83.
45. de Oliveira, T.; Deforche, K.; Cassol, S.; Salminem, M.; Paraskevis, D.; Seebregts, C.; Snoeck, J.; van Rensburg, E.J.; Wensing, A.M.J.; van de Vijver, D.A.; Boucher, C.A.; Camacho, R.; Vandamme, A.-M. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005, 21, 3797-3800. BioAfrica.net. Available online: http://bioafrica.mrc.ac.za/ (accessed on 31 July 2010).
46. Bruen, T.C.; Philippe, H.; Bryant, D., A simple and robust statistical test for detecting the presence of recombination. Genetics 2006, 172, 2665-2681.
47. Boni, M.F.; Posada, D.; Feldman, M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 2007, 176, 1035-1047.
48. Huson, D.H.; Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23, 254-267.
49. Drummond, A.J.; Nicholls, G.K.; Rodrigo, A.G.; Solomon, W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 2002, 161, 1307-1320.
50. Van Dooren, S.; Pybus, O.G.; Salemi, M.; Liu, H.-F.; Goubau, P.; Remondegui, C.; Talarmin, A.; Gotuzzo, E.; Alcantara, L.C.J.; Galvão-Castro, B. The low evolutionary rate of human T-cell lymphotropic virus type-1 confirmed by analysis of vertical transmission chains. Mol. Biol. Evol. 2004, 21, 603-611.
51. Rambaut, A.; Drummond, A. Tracer, version 1.5. Available online: http://beast.bio.ed.ac.uk/Tracer (accessed on 30 November 2009).
52. Rambaut, A. FigTree, version 1.3.1. Available online: http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 21 December 2009).
53. Lemey, P.; Pybus, O.G.; Rambaut, A.; Drummond, A.J.; Robertson, D.L.; Roques, P.; Worobey, M.; Vandamme, A.M. The molecular population genetics of HIV-1 group O. Genetics 2004, 167, 1059-1068.
54. Suchard, M.A.; Weiss, R.E.; Sinsheimer, J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 2001, 18, 1001-1013.