Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

Journal of Virology

Volumn 78, Issue 5, 2004, Pages 2537-2544

  Radjef, Nadjia ^a,c   Gordien, Emmanuel ^a,c   Ivaniushina, Valeria ^d   Gault, Elyanne ^a,c   Anaïs, Patricia ^a,c   Drugan, Tudor ^e   Trinchet, Jean Claude ^b   Roulot, Dominique ^b   Tamby, Mathieu ^a,c   Milinkovitch, Michel C ^f   Dény, Paul ^a,c  

^a AVICENNE HOSPITAL   (France)

^b Service d'Hepato Gastroenterologie   (France)

^c UNIVERSITÉ PARIS 13   (France)

^d Institute of Influenza   (Russian Federation)

^e IULIU HATIEGANU UNIVERSITY OF MEDICINE AND PHARMACY   (Romania)

^f FREE UNIVERSITY OF BRUSSELS   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; VIRUS DNA; VIRUS RNA;

ADOLESCENT; ADULT; AFRICA; ARTICLE; FEMALE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HEPATITIS B VIRUS; HEPATITIS DELTA VIRUS; HISTOLOGY; HUMAN; HUMAN TISSUE; LIVER CIRRHOSIS; MAJOR CLINICAL STUDY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS GENOME; VIRUS HEPATITIS; VIRUS INFECTION; VIRUS TRANSMISSION;

DELTAVIRUS;

ADOLESCENT; ADULT; AFRICA; AMINO ACID SEQUENCE; BASE SEQUENCE; EVOLUTION, MOLECULAR; FEMALE; GENOME, VIRAL; GENOTYPE; GEOGRAPHY; HELPER VIRUSES; HEPATITIS B VIRUS; HEPATITIS DELTA VIRUS; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, VIRAL;

EID: 10744229986     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.78.5.2537-2544.2004     Document Type: Article

References (46)

1. Brazas, R., and D. Ganem. 1996. A cellular homolog of hepatitis delta antigen: implications for viral replication and evolution. Science 274:90-94.
2. Casey, J. L. 1996. Hepatitis delta virus. Genetics and pathogenesis. Clin. Lab. Med. 16:451-464.
3. Casey, J. L., T. B. Brown, F. S. Wignall, and J. L. Gerin. 1993. A genotype of hepatitis delta virus that occurs in northern South America. Proc. Natl. Acad. Sci. USA 90:9016-9020.
4. Casey, J. L., and J. L. Gerin. 1998. Genotype-specific complementation of hepatitis delta virus RNA replication by hepatitis delta antigen. J. Virol. 72:2806-2814.
5. Chang, F.-L., P.-J. Chen, S.-J. Tu, C.-J. Wang, and D.-S. Chen. 1991. The large form of hepatitis 8 antigen is crucial for assembly of hepatitis 8 virus. Proc. Natl. Acad. Sci. USA 88:8490-8494.
6. Chao, Y. C., M. F. Chang, I. Gust, and M. M. Lai. 1990. Sequence conservation and divergence of hepatitis delta virus RNA. Virology 178:384-392.
7. Dény, P., G. Fattovich, F. Le Gal, G. Giustina, C. Lecot, G. Morsica, H. Poinsot, A. Alberti, and C. Brechot. 1994. Polymerase-chain-reaction-based semi-quantification of hepatitis D viraemia in patients treated with high doses of alpha 2b interferon. Res. Virol. 145:287-295.
8. Dieye, A., V. Obami-Itou, M. F. Barry, G. Raphenon, A. Thiam, R. Ndiaye, M. Ndiaye, M. L. Diaw, and L. Diakhate. 1999. Association between class 1 HLA alleles and HBs antigen carrier status among blood donors in Senegal. Dakar Med. 44:166-170.
9. Dumpis, U., E. C. Holmes, M. Mendy, A. Hill, M. Thursz, A. Hall, H. Whittle, and P. Karayiannis. 2001. Transmission of hepatitis B virus infection in Gambian families revealed by phylogenetic analysis. J. Hepatol. 35:99-104.
10. Elena, S. F., J. Dopazo, B. Flores, T. O. Diener, and A. Moya. 1991. Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA. Proc. Natl. Acad. Sci. USA 88:5631-5634.
11. Fares, M. A., and E. C. Holmes. 2002. A revised evolutionary history of hepatitis B virus (HBV). J. Mol. Evol. 54:807-814.
12. Gaeta, G. B., T. Stroffolini, M. Chiaramonte, T. Ascione, G. Stornaiuolo, S. Lobello, E. Sagnelli, M. R. Brunetto, and M. Rizzetto. 2000. Chronic hepatitis D: a vanishing disease? An Italian multicenter study. Hepatology 32:824-827.
13. Imazeki, F., M. Omata, and M. Ohto. 1991. Complete nucleotide sequence of hepatitis delta virus RNA in Japan. Nuclleic Acids Res. 19:5439-5440.
14. Ivaniushina, V., N. Radjef, M. Alexeeva, E. Gault, S. Semenov, M. Salhi, O. Kiselev, and P. Deny. 2001. Hepatitis delta virus genotypes I and II cocirculate in an endemic area of Yakutia, Russia. J. Gen. Virol. 82:2709-2718.
15. Jenkins, G. M., C. H. Woelk, A. Rambaut, and E. C. Holmes. 2000. Testing the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus. J. Mol. Evol. 50:98-102.
16. Lanford, R. E., D. Chavez, K. M. Brasky, R. B. Burns III, and R. Rico-Hesse. 1998. Isolation of a hepadnavirus from the woolly monkey, a New World primate. Proc. Natl. Acad. Sci. USA 95:5757-5761.
17. Lee, C. M., C. S. Changchien, J. C. Chung, and Y. F. Liaw. 1996. Characterization of a new genotype II hepatitis delta virus from Taiwan. J. Med. Virol. 49:145-154.
18. Lemmon, A., and M. Milinkovitch. 2002. The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. USA 99:10516-10521.
19. Lin, F. M., C. M. Lee, T. C. Wang, and M. Chao. 2003. Initiation of RNA replication of cloned Taiwan-3 isolate of hepatitis delta virus genotype II in cultured cells. Biochem. Biophys. Res. Commun. 306:966-972.
20. Long, M., S. J. de Souza, and W. Gilbert. 1997. Delta-interacting protein A and the origin of hepatitis delta antigen. Science 276:824-825.
21. Loytynoja, A., and M. C. Milinkovitch. 2003. A hidden Markov model for progressive multiple alignment. Bioinformatics 19:1505-1513.
22. Loytynoja, A., and M. C. Milinkovitch. 2001. SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17:573-574.
23. Luo, G. X., M. Chao, S. Y. Hsieh, C. Sureau, K. Nishikura, and J. Taylor. 1990. A specific base transition occurs on replicating hepatitis delta virus RNA. J. Virol. 64:1021-1027.
24. Ma, S.-P., H. Sakugawa, Y. Makino, M. Tadano, F. Kinjo, and A. Saito. 2003. The complete genomic sequence of hepatitis delta virus genotype IIb prevalent in Okinawa, Japan. J. Gen. Virol. 84:461-464.
25. MacDonald, D. M., E. C. Holmes, J. C. Lewis, and P. Simmonds. 2000. Detection of hepatitis B virus infection in wild-born chimpanzees (Pan troglodytes versus): phylogenetic relationships with human and other primate genotypes. J. Virol. 74:4253-4257.
26. Morice, Y., D. Roulot, V. Grando, J. Stirnemann, E. Gault, V. Jeantils, M. Bentata, B. Jarrousse, O. Lortholary, C. Pallier, and P. Deny. 2001. Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns. J. Gen. Virol. 82:1001-1012.
27. Nakano, T., C. N. Shapiro, S. C. Hadler, J. L. Casey, M. Mizokami, E. Orito, and B. H. Robertson. 2001. Characterization of hepatitis D virus genotype III among Yucpa Indians in Venezuela. J. Gen. Virol. 82:2183-2189.
28. Niro, G. A., J. L. Casey, E. Gravinese, M. Garrubba, P. Conoscitore, E. Sagnelli, M. Durazzo, N. Caporaso, F. Perri, G. Leandro, D. Facciorusso, M. Rizzetto, and A. Andriulli. 1999. Intrafamilial transmission of hepatitis delta virus: molecular evidence. J. Hepatol. 30:564-569.
29. Parana, R., F. Gerard, J. L. Lesbordes, C. Pichoud, L. Vitvitski, L. G. Lyra, and C. Trepo. 1995. Serial transmission of spongiocytic hepatitis to woodchucks (possible association with a specific delta strain). J. Hepatol. 22:468-473.
30. Rizzetto, M., M. Canese, and S. Arico. 1977. Immunofluorescence detection of a new antigen antibody system (Delta/anti-Delta) associated to hepatitis B virus in liver and serum of HBs Ag carriers. Gut 18:997-1003.
31. Rizzetto, M., and M. Durazzo. 1991. Hepatitis delta virus (HDV) infections. Epidemiological and clinical heterogeneity. J. Hepatol. 13:S116-S118.
32. Robertson, B. H., and H. S. Margolis. 2002. Primate hepatitis B viruses-genetic diversity, geography and evolution. Rev. Med. Virol. 12:133-141.
33. Sakugawa, H., H. Nakasone, T. Nakayoshi, Y. Kawakami, S. Miyazato, F. Kinjo, A. Saito, S. P. Ma, H. Hotta, and M. Kinoshita. 1999. Hepatitis delta virus genotype IIb predominates in an endemic area, Okinawa, Japan. J. Med. Virol. 58:366-372.
34. Shakil, A. O., S. Hadziyannis, J. H. Hoofnagle, A. M. Di Bisceglie, J. L. Gerin, and J. L. Casey. 1997. Geographic distribution and genetic variability of hepatitis delta virus genotype I. Virology 234:160-167.
35. Stuyver, L., S. De Gendt, C. Van Geyt, F. Zoulim, M. Fried, R. F. Schinazi, and R. Rossau. 2000. A new genotype of hepatitis B virus: complete genome and phylogenetic relatedness. J. Gen. Virol. 81:67-74.
36. Sugimoto, C., T. Kitamura, J. Guo, M. N. Al-Ahdal, S. N. Shchelkunov, B. Otova, P. Ondrejka, J. Y. Chollet, S. El-Safi, M. Ettayebi, G. Gresenguet, T. Kocagoz, S. Chaiyarasamee, K. Z. Thant, S. Thein, K. Moe, N. Kobayashi, F. Taguchi, and Y. Yogo. 1997. Typing of urinary JC virus DNA offers a novel means of tracing human migrations. Proc. Natl. Acad. Sci. USA 94:9191-9196.
37. Sureau, C., B. Guerra, and R. E. Lanford. 1993. Role of the large hepatitis B virus envelope protein in infectivity of the hepatitis delta virion. J. Virol. 67:366-372.
38. Swofford, D. 1998. PAUP*: Phylogenetic Analysis Using Parsimony (and other methods), version 4.0d64 (in progress). Sinauer Associates, Sunderland, Mass.
39. Taylor, J. M. 2003. Replication of human hepatitis delta virus: recent developments. Trends Microbiol. 11:185-190.
40. Vanden Haesevelde, M., J. L. Decourt, R. J. De Leys, B. Vanderborght, G. van der Groen, H. van Heuverswijn, and E. Saman. 1994. Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J. Virol. 68:1586-1596.
41. Wang, K.-S., Q.-L. Choo, A. J. Weiner, J.-H. Ou, R. C. Najarian, R. M. Thayer, G. T. Mullenbach, K. J. Denniston, J. L. Gerin, and M. Houghton. 1986. Structure, sequence and expression of the hepatitis delta (δ) viral genome. Nature 323:508-514. (Erratum, 328:456, 1987.)
42. Wang, T. C., and M. Chao. 2003. Molecular cloning and expression of the hepatitis delta virus genotype IIb genome. Biochem. Biophys. Res. Commun. 303:357-363.
43. Weiner, A., Q.-L. Choo, K.-S. Wang, S. Govindarajan, A. Redeker, J. Gerin, and M. Houghton. 1988. A single antigenomic open reading frame of the hepatitis delta virus encodes the epitope(s) of both hepatitis delta antigen polypeptides p24δ and p27δ. J. Virol. 62:594-599.
44. Wu, J. C., T. Y. Chiang, and I. J. Sheen. 1998. Characterization and phylogenetic analysis of a novel hepatitis D virus strain discovered by restriction fragment length polymorphism analysis. J. Gen. Virol. 79:1105-1113.
45. Yamaguchi, Y., J. Filipovska, K. Yano, A. Furuya, N. Inukai, T. Narita, T. Wada, S. Sugimoto, M. M. Konarska, and H. Handa. 2001. Stimulation of RNA polymerase II elongation by hepatitis delta antigen. Science 293:124-127.
46. Zhang, Y. Y., E. Tsega, and B. G. Hansson. 1996. Phylogenetic analysis of hepatitis D viruses indicating a new genotype I subgroup among African isolates. J. Clin. Microbiol. 34:3023-3030.