The first full-length endogenous hepadnaviruses: Identification and analysis

Journal of Virology

Volumn 86, Issue 17, 2012, Pages 9510-9513

  Liu, Wei ^a   Pan, Shaokun ^a   Yang, Huijuan ^a   Bai, Weiya ^a   Shen, Zhongliang ^a   Liu, Jing ^a   Xie, Youhua ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC SCREENING; GENOME ANALYSIS; HEPADNAVIRUS; HEPATITIS B VIRUS; MELOPSITTACUS UNDULATUS; MOLECULAR DYNAMICS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAKEET; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TAXONOMIC IDENTIFICATION; TAXONOMIC RANK; VIRUS GENOME;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; GENOME, VIRAL; HEPADNAVIRIDAE; HEPADNAVIRIDAE INFECTIONS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROVIRUSES; SEQUENCE ALIGNMENT; VIRAL PROTEINS;

HEPATITIS B VIRUS; MELOPSITTACUS; MELOPSITTACUS UNDULATUS; METAZOA;

EID: 84866167988     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01164-12     Document Type: Article

References (26)

1. Beck J, Nassal M. 2007. Hepatitis B virus replication. World J. Gastroenterol.. 13: 48-64.
2. Cui J, Holmes EC. 2012. Endogenous lentiviruses in the ferret genome. J. Virol.. 86: 3383-3385.
3. Dejean A, Sonigo P, Wain-Hobson S, Tiollais P. 1984. Specific hepatitis B virus integration in hepatocellular carcinoma DNA through a viral 11-base-pair direct repeat. Proc. Natl. Acad. Sci. U. S. A.. 81: 5350-5354.
4. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res.. 32: 1792-1797.
5. Emerman M, Malik HS. 2010. Paleovirology-modern consequences of ancient viruses. PLoS Biol. 8:e1000301. doi:10.1371/journal.pbio. 1000301.
6. Gifford RJ, et al. 2008. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl. Acad. Sci. U. S. A.. 105: 20362-20367.
7. Gilbert C, Feschotte C. 2010. Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol. 8:e1000495. doi:10.1371/ journal.pbio.1000495.
8. Gilbert C, Maxfield DG, Goodman SM, Feschotte C. 2009. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet. 5:e1000425. doi:10.1371/journal.pgen.1000425.
9. Guerrero RB, Roberts LR. 2005. The role of hepatitis B virus integrations in the pathogenesis of human hepatocellular carcinoma. J. Hepatol.. 42: 760-777.
10. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol.. 59: 307-321.
11. Hino O, Ohtake K, Rogler CE. 1989. Features of two hepatitis B virus (HBV) DNA integrations suggest mechanisms of HBV integration. J. Virol.. 63: 2638-2643.
12. Johnson WE, Coffin JM. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl. Acad. Sci. U. S. A.. 96: 10254-10260.
13. Katzourakis A, Gifford RJ. 2010. Endogenous viral elements in animal genomes. PLoS Genet. 6:e1001191. doi:10.1371/journal.pgen.1001191.
14. Katzourakis A, Tristem M, Pybus OG, Gifford RJ. 2007. Discovery and analysis of the first endogenous lentivirus. Proc. Natl. Acad. Sci. U. S. A.. 104: 6261-6265.
15. Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A. 2009. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology. 384: 7-11.
16. Koshy R, et al. 1983. Integration of hepatitis B virus DNA: evidence for integration in the single-stranded gap. Cell. 34: 215-223.
17. Matsubara K, Tokino T. 1990. Integration of hepatitis B virus DNA and its implications for hepatocarcinogenesis. Mol. Biol. Med.. 7: 243-260.
18. Nguyen DH, Ludgate L, Hu J. 2008. Hepatitis B virus-cell interactions and pathogenesis. J. Cell. Physiol.. 216: 289-294.
19. Patel MR, Emerman M, Malik HS. 2011. Paleovirology-ghosts and gifts of viruses past. Curr. Opin. Virol.. 1: 304-309.
20. Piasecki T, et al. 2012. Molecular characterisation of an avihepadnavirus isolated from Psittacula krameri (ring-necked parrot). Arch. Virol.. 157: 585-590.
21. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol.. 25: 1253-1256.
22. Schaefer S. 2007. Hepatitis B virus taxonomy and hepatitis B virus genotypes. World J. Gastroenterol.. 13: 14-21.
23. Seeger C, Mason WS. 2000. Hepatitis B virus biology. Microbiol. Mol. Biol. Rev.. 64: 51-68.
24. van der Loo W, Abrantes J, Esteves PJ. 2009. Sharing of endogenous lentiviral gene fragments among leporid lineages separated for more than 12 million years. J. Virol.. 83: 2386-2388.
25. Zhou Y, Holmes EC. 2007. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J. Mol. Evol.. 65: 197-205.
26. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res.. 31: 3406-3415.