Virus Genes

, 40:60 | Cite as

Comparative analysis of American Dengue virus type 1 full-genome sequences

  • S. E. S. Carvalho
  • D. P. Martin
  • L. M. Oliveira
  • B. M. Ribeiro
  • T. Nagata
Article

Abstract

Dengue virus (DENV; Genus Flavivirus, Family Flaviviridae) has been circulating in Brazil since at least the mid-1980s and continues to be responsible for sporadic cases of Dengue fever and Dengue hemorrhagic fever throughout this country. Here, we describe the full genomes of two new Brazilian DENV-serotype 1 (DENV-1) variants and analyze these together with all other available American DENV-1 full-genome sequences. Besides confirming the existence of various country-specific DENV-1 founder effects that have produced a high degree of geographical structure in the American DENV-1 population, we also identify that one of the new viruses is one of only three detectable intra-American DENV-1 recombinants. Although such obvious evidence of genetic exchange among epidemiologically unlinked Latin American DENV-1 sequences is relatively rare, we find that at the population-scale there exists substantial evidence of pervasive recombination that most likely occurs between viruses that are so genetically similar that it is not possible to reliably distinguish and characterize individual recombination events.

Keywords

Molecular epidemiology Dengue fever Arbovirus Geographic distribution Virus recombination 

Notes

Acknowledgments

The study was financially supported by Universidade Católica de Brasília. S.E.S.C. was supported by the “Conselho de Desenvolvimento Cientifico” (CNPq, Brazil) Doctoral program. We thank Dr. Matthew Henn (Broad Institute of MIT and Harvard), Dr. Jorge Munoz (Centers for Disease Control, Puerto Rico), Dr. Irene Bosch (University of Massachusetts Medical School), Dr. Eva Harris (University of California Berkeley), and Dr. Guillermo Comach (Universidad de Carabobo, Venezuela) for generously allowing us to use unpublished DENV-1 full-genome sequences that have been generated under the Broad Institute’s NIAID Microbial Sequencing Center Genome Resources in Dengue Consortium (GRID) dengue genome project (http://www.broad.mit.edu/annotation/viral/Dengue/Home.html).

Supplementary material

11262_2009_428_MOESM1_ESM.doc (32 kb)
Supplementary material 1 (DOC 33 kb)

References

  1. 1.
    D.J. Gubler, Emerg. Infect. Dis. 4, 442–450 (1998)CrossRefPubMedGoogle Scholar
  2. 2.
    M.G. Guzman, G. Kouri, Lancet Infect. Dis. 2, 33–42 (2002)CrossRefPubMedGoogle Scholar
  3. 3.
  4. 4.
    B.D. Lindenbach, C.M. Rice, Adv. Virus Res. 59, 23–61 (2003)CrossRefPubMedGoogle Scholar
  5. 5.
    D.J. Gubler, M. Meltzer, Adv. Virus Res. 53, 35–70 (1999)CrossRefPubMedGoogle Scholar
  6. 6.
    C.N. dos Santos, C.F. Rocha, M. Cordeiro, S.P. Fragoso, F. Rey, V. Deubel, P. Despres, Virus Res. 90, 197–205 (2002)CrossRefPubMedGoogle Scholar
  7. 7.
    P. Van der Stuyft, A. Gianella, M. Pirard, A. Holzman, C. Peredo, M. Boelaert, V. Vorndam, Trop. Med. Int. Health 3, 857–858 (1998)CrossRefPubMedGoogle Scholar
  8. 8.
    G. Avilés, G. Rangeón, V. Vorndam, A. Briones, P. Baroni, D. Enria, M.S. Sabattini, Emerg. Infect. Dis. 5, 575–578 (1999)CrossRefPubMedGoogle Scholar
  9. 9.
    G. Aviles, J. Rowe, J. Meissner, J.C. Manzur Caffarena, D. Enria, S. St Jeor, Arch. Virol. 147, 2075–2087 (2002)CrossRefPubMedGoogle Scholar
  10. 10.
    P.R. Barrero, A.S. Mistchenko, Virus Res. 101, 135–145 (2004)CrossRefPubMedGoogle Scholar
  11. 11.
    R.M. Nogueira, M.P. Miagostovich, E. Lampe, R.W. Souza, S.M. Zagne, H.G. Schatzmayr, Epidemiol. Infect. 111, 163–170 (1993)CrossRefPubMedGoogle Scholar
  12. 12.
    M.P. Miagostovich, F.B. dos Santos, T.S. de Simone, E.V. Costa, A.M. Filippis, H.G. Schatzmayr, R.M. Nogueira, Braz. J. Med. Biol. Res. 35, 869–872 (2002)CrossRefPubMedGoogle Scholar
  13. 13.
    W.B. Messer, D.J. Gubler, E. Harris, K. Sivananthan, A.M. de Silva, Emerg. Infect. Dis. 9, 800–809 (2003)PubMedGoogle Scholar
  14. 14.
    K.C. Leitmeyer, D.W. Vaughn, D.M. Watts, R. Salas, I. Villalobos, C.C. Ramos, R. Rico-Hesse, J. Virol. 73, 4738–4747 (1999)PubMedGoogle Scholar
  15. 15.
    C.C. King, D.Y. Chao, L.J. Chien, G.J. Chang, T.H. Lin, Y.C. Wu, J.H. Huang, Virol. J. 5, 63 (2008)CrossRefPubMedGoogle Scholar
  16. 16.
    H.J. Tolou, P. Couissinier-Paris, J.P. Durand, V. Mercier, J.J. de Pina, P. de Micco, F. Billoir, R.N. Charrel, X. de Lamballerie, J. Gen. Virol. 82, 1283–1290 (2001)PubMedGoogle Scholar
  17. 17.
    E.C. Holmes, M. Worobey, A. Rambaut, Mol. Biol. Evol. 16, 405–409 (1999)PubMedGoogle Scholar
  18. 18.
    P.D. Copper, A. Steiner-Pryor, P.D. Scotti, D. Delong, J. Gen. Virol. 23, 41–49 (1974)CrossRefPubMedGoogle Scholar
  19. 19.
    C.S. Hahn, S. Lustig, E.G. Strauss, J.H. Strauss, Proc. Natl Acad. Sci. USA 85, 5997–6001 (1988)CrossRefPubMedGoogle Scholar
  20. 20.
    R. Rico-Hesse, Virology 174, 479–493 (1990)CrossRefPubMedGoogle Scholar
  21. 21.
    J. Blok, A.J. Gibbs, S.M. McWilliam, U.T. Vitarana, Arch. Virol. 118, 209–223 (1991)CrossRefPubMedGoogle Scholar
  22. 22.
    V. Deubel, R.M. Nogueira, M.T. Drouet, H. Zeller, J.M. Reynes, D.Q. Ha, Arch. Virol. 129, 197–210 (1993)CrossRefPubMedGoogle Scholar
  23. 23.
    J.A. Lewis, G.J. Chang, R.S. Lanciotti, R.M. Kinney, L.M. Mayer, D.W. Trent, Virology 197, 216–224 (1993)CrossRefPubMedGoogle Scholar
  24. 24.
    R.S. Lanciotti, J.G. Lewis, D.J. Gubler, D.W. Trent, J. Gen. Virol. 75, 65–75 (1994)CrossRefPubMedGoogle Scholar
  25. 25.
    E. Chungue, O. Cassar, M.T. Drouet, M.G. Guzman, M. Laille, L. Rosen, V.J. Deubel, J. Gen. Virol. 76, 1877–1884 (1995)CrossRefPubMedGoogle Scholar
  26. 26.
    K. Bundo, A. Igarashi, J. Virol. Methods 11, 15–22 (1985)CrossRefPubMedGoogle Scholar
  27. 27.
    E.A. Henchal, M.K. Gentry, J.M. McCown, W.E. Brandt, Am. J. Trop. Med. Hyg. 31, 830–836 (1982)PubMedGoogle Scholar
  28. 28.
    J.K. Bonfield, K. Smith, R. Staden, Nucleic Acids Res. 23, 4992–4999 (1995)CrossRefPubMedGoogle Scholar
  29. 29.
    J.D. Thompson, D.G. Higgins, T.J. Gibson, Nucleic Acids Res. 22, 4673–4680 (1994)CrossRefPubMedGoogle Scholar
  30. 30.
    S. Guindon, O. Gascuel, Syst. Biol. 52, 696–704 (2003)CrossRefPubMedGoogle Scholar
  31. 31.
    D.P. Martin, C. Williamson, D. Posada, Bioinformatics 21, 260–262 (2005)CrossRefPubMedGoogle Scholar
  32. 32.
    D. Martin, E. Rybicki, Bioinformatics 16, 562–563 (2000)CrossRefPubMedGoogle Scholar
  33. 33.
    M. Padidam, S. Sawyer, C.M. Fauquet, Virology 265, 218–225 (1999)CrossRefPubMedGoogle Scholar
  34. 34.
    D.P. Martin, D. Posada, K.A. Crandall, C. Williamson, AIDS Res. Hum. Retroviruses 21, 98–102 (2005)CrossRefPubMedGoogle Scholar
  35. 35.
    J.M. Smith, J. Mol. Evol. 34, 126–129 (1992)PubMedGoogle Scholar
  36. 36.
    M.J. Gibbs, J.S. Armstrong, A.J. Gibbs, Bioinformatics 16, 573–582 (2000)CrossRefPubMedGoogle Scholar
  37. 37.
    M.F. Boni, D. Posada, M.W. Feldman, Genetics 176, 1035–1047 (2007)CrossRefPubMedGoogle Scholar
  38. 38.
    L. Heath, E. van der Walt, A. Varsani, D.P. Martin, J. Virol. 80, 11827–11832 (2006)CrossRefPubMedGoogle Scholar
  39. 39.
    G. McVean, P. Awadalla, P. Fearnhead, Genetics 160, 1231–1241 (2002)PubMedGoogle Scholar
  40. 40.
    G.A. McVean, S.R. Myers, S. Hunt, P. Deloukas, D.R. Bentley, P. Donnelly, Science 304, 581–584 (2004)CrossRefPubMedGoogle Scholar
  41. 41.
    A. Carvajal-Rodriguez, K.A. Crandall, D. Posada, Mol. Biol. Evol. 23, 817–827 (2006)CrossRefPubMedGoogle Scholar
  42. 42.
    S.S. Twiddy, E.C. Holmes, A. Rambaut, Mol. Biol. Evol. 20, 122–129 (2003)CrossRefPubMedGoogle Scholar
  43. 43.
    H.G. Schatzmayr, R.M. Nogueira, A.P.T. Rosa, Mem. Inst. Oswaldo Cruz 81, 245–246 (1986)CrossRefPubMedGoogle Scholar
  44. 44.
    R.M. Nogueira, M.P. Miagostovich, H.G. Schatzmayr, Cad Saude Publica 16, 205–211 (2000)CrossRefPubMedGoogle Scholar
  45. 45.
    K.P. Coyne, F.C. Reed, C.J. Porter, S. Dawson, R.M. Gaskell, A.D. Radford, J. Gen. Virol. 87, 921–926 (2006)CrossRefPubMedGoogle Scholar
  46. 46.
    R. Colina, D. Casane, S. Vasquez, L. Garcia-Aguirre, A. Chunga, H. Romero, B. Khan, J. Cristina, J. Gen. Virol. 85, 31–37 (2004)CrossRefPubMedGoogle Scholar
  47. 47.
    M.J. Stanhope, J.R. Brown, H. Amrine-Madsen, Infect. Genet. Evol. 4, 15–19 (2004)CrossRefPubMedGoogle Scholar
  48. 48.
    E.R. Chare, E.C. Holmes, Arch. Virol. 151, 933–946 (2006)CrossRefPubMedGoogle Scholar
  49. 49.
    D. Posada, K.A. Crandall, Proc. Natl Acad. Sci. USA 98, 13757–13762 (2001)CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • S. E. S. Carvalho
    • 1
  • D. P. Martin
    • 2
  • L. M. Oliveira
    • 3
  • B. M. Ribeiro
    • 1
  • T. Nagata
    • 1
    • 3
  1. 1.Program of Molecular Pathology and Department of Cell Biology, Electron Microscopy and Virology LaboratoryUniversidade de Brasília BrasíliaBrasil
  2. 2.Institute of Infectious Disease and Molecular MedicineUniversity of Cape Town, ObservatoryCape TownSouth Africa
  3. 3.Program of Genomic Science and BiotechnologyUniversidade Católica de Brasília BrasíliaBrasil

Personalised recommendations