1887

Abstract

The complete nucleotide sequences of eight (HEV-B) strains were determined, representing five serotypes, E6, E7, E11, CVB3 and CVB5, which were isolated in the former Soviet Union between 1998 and 2002. All strains were mosaic recombinants and only the VP2–VP3–VP1 genome region was similar to that of the corresponding prototype HEV-B strains. In seven of the eight strains studied, the 2C–3D genome region was most similar to the prototype E30, EV74 and EV75 strains, whilst the remaining strain was most similar to the prototype E1 and E9 strains in the non-structural protein genome region. Most viruses also bore marks of additional recombination events in this part of the genome. In the 5′ non-translated region, all strains were more similar to the prototype E9 than to other enteroviruses. In most cases, recombination mapped to the VP4 and 2ABC genome regions. This, together with the star-like topology of the phylogenetic trees for these genome regions, identified these genome parts as recombination hot spots. These findings further support the concept of independent evolution of enterovirus genome fragments and indicate a requirement for more advanced typing approaches. A range of available phylogenetic methods was also compared for efficient detection of recombination in enteroviruses.

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2005-12-01
2019-11-12
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References

  1. Blomquist, S., Bruu, A.-L., Stenvik, M. & Hovi, T. ( 2003; ). Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1. J Gen Virol 84, 573–580.[CrossRef]
    [Google Scholar]
  2. Brown, B., Oberste, M. S., Maher, K. & Pallansch, M. A. ( 2003; ). Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region. J Virol 77, 8973–8984.[CrossRef]
    [Google Scholar]
  3. Cammack, N., Phillips, A., Dunn, G., Patel, V. & Minor, P. D. ( 1988; ). Intertypic genomic rearrangements of poliovirus strains in vaccinees. Virology 167, 507–514.[CrossRef]
    [Google Scholar]
  4. Chevaliez, S., Szendröi, A., Caro, V., Balanant, J., Guillot, S., Berencsi, G. & Delpeyroux, F. ( 2004; ). Molecular comparison of echovirus 11 strains circulating in Europe during an epidemic of multisystem hemorrhagic disease of infants indicates that evolution generally occurs by recombination. Virology 325, 56–70.[CrossRef]
    [Google Scholar]
  5. Dahourou, G., Guillot, S., Le Gall, O. & Crainic, R. ( 2002; ). Genetic recombination in wild-type poliovirus. J Gen Virol 83, 3103–3110.
    [Google Scholar]
  6. Furione, M., Guillot, S., Otelea, D., Balanant, J., Candrea, A. & Crainic, R. ( 1993; ). Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology 196, 199–208.[CrossRef]
    [Google Scholar]
  7. Gavrilin, G. V., Cherkasova, E. A., Lipskaya, G. Y., Kew, O. M. & Agol, V. I. ( 2000; ). Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model. J Virol 74, 7381–7390.[CrossRef]
    [Google Scholar]
  8. Georgescu, M.-M., Delpeyroux, F., Tardy-Panit, M., Balanant, J., Combiescu, M., Combiescu, A. A., Guillot, S. & Crainic, R. ( 1994; ). High diversity of poliovirus strains isolated from the central nervous system from patients with vaccine-associated paralytic poliomyelitis. J Virol 68, 8089–8101.
    [Google Scholar]
  9. Georgescu, M.-M., Delpeyroux, F. & Crainic, R. ( 1995; ). Tripartite genome organization of a natural type 2 vaccine/nonvaccine recombinant poliovirus. J Gen Virol 76, 2343–2348.[CrossRef]
    [Google Scholar]
  10. Gmyl, A. P., Korshenko, S. A., Belousov, E. V., Khitrina, E. V. & Agol, V. I. ( 2003; ). Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9, 1221–1231.[CrossRef]
    [Google Scholar]
  11. Gromeier, M., Wimmer, E. & Gorbalenya, A. E. ( 1999; ). Genetics, pathogenesis and evolution of picornaviruses. In Origin and Evolution of Viruses, pp. 287–343. Edited by E. Domingo, R. Webster & J. Holland. London: Academic Press.
  12. Guillot, S., Caro, V., Cuervo, N., Korotkova, E., Combiescu, M., Persu, A., Aubert-Combiescu, A., Delpeyroux, F. & Crainic, R. ( 2000; ). Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J Virol 74, 8434–8443.[CrossRef]
    [Google Scholar]
  13. Husmeier, D. & Wright, F. ( 2001; ). Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17 (Suppl. 1), S123–S131.[CrossRef]
    [Google Scholar]
  14. Iizuka, N., Kuge, S. & Nomoto, A. ( 1987; ). Complete nucleotide sequence of the genome of coxsackievirus B1. Virology 156, 64–73.[CrossRef]
    [Google Scholar]
  15. Kirkegaard, K. & Baltimore, D. ( 1986; ). The mechanism of RNA recombination in poliovirus. Cell 47, 433–443.[CrossRef]
    [Google Scholar]
  16. Lindberg, A. M., Johansson, S. & Andersson, A. ( 1999; ). Echovirus 5: infectious transcripts and complete nucleotide sequence from uncloned cDNA. Virus Res 59, 75–87.[CrossRef]
    [Google Scholar]
  17. Lindberg, M. A., Andersson, P., Savolainen, C., Mulders, M. N. & Hovi, T. ( 2003; ). Evolution of the genome of Human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. J Gen Virol 84, 1223–1235.[CrossRef]
    [Google Scholar]
  18. Lipskaya, G. Y., Muzychenko, A. R., Kutitova, O. K., Maslova, S. V., Equestre, M., Drozdov, S. G., Perez Bercoff, R. & Agol, V. I. ( 1991; ). Frequent isolation of intertypic poliovirus recombinants with serotype 2 specificity from vaccine-associated polio cases. J Med Virol 35, 290–296.[CrossRef]
    [Google Scholar]
  19. Lukashev, A. N. ( 2005; ). Role of recombination in evolution of enteroviruses. Rev Med Virol 15, 157–167.[CrossRef]
    [Google Scholar]
  20. Lukashev, A. N., Lashkevich, V. A., Ivanova, O. E., Koroleva, G. A., Hinkkanen, A. E. & Ilonen, J. ( 2003; ). Recombination in circulating enteroviruses. J Virol 77, 10423–10431.[CrossRef]
    [Google Scholar]
  21. Lukashev, A. N., Lashkevich, V. A., Koroleva, G. A., Ilonen, J. & Hinkkanen, A. E. ( 2004; ). Recombination in uveitis-causing enterovirus strains. J Gen Virol 85, 463–470.[CrossRef]
    [Google Scholar]
  22. Macadam, A. J., Arnold, C., Howlett, J. & 9 other authors ( 1989; ). Reversion of the attenuated and temperature-sensitive phenotypes of the Sabin type 3 strain of poliovirus in vaccinees. Virology 172, 408–414.[CrossRef]
    [Google Scholar]
  23. McGuire, G. & Wright, F. ( 2000; ). topal 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics 16, 130–134.[CrossRef]
    [Google Scholar]
  24. Milne, I., Wright, F., Rowe, G., Marshall, D. F., Husmeier, D. & McGuire, G. ( 2004; ). topali: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20, 1806–1807.[CrossRef]
    [Google Scholar]
  25. Minor, P. D., John, A., Ferguson, M. & Icenogle, J. P. ( 1986; ). Antigenic and molecular evolution of the vaccine strain of type 3 poliovirus during the period of excretion by a primary vaccinee. J Gen Virol 67, 693–706.[CrossRef]
    [Google Scholar]
  26. Oberste, M. S., Maher, K. & Pallansch, M. A. ( 2004a; ). Evidence for frequent recombination within species Human enterovirus B based on complete genomic sequences of all thirty-seven serotypes. J Virol 78, 855–867.[CrossRef]
    [Google Scholar]
  27. Oberste, M. S., Michele, S. M., Maher, K. & 11 other authors ( 2004b; ). Molecular identification and characterization of two proposed new enterovirus serotypes, EV74 and EV75. J Gen Virol 85, 3205–3212.[CrossRef]
    [Google Scholar]
  28. Oberste, M. S., Peñaranda, S., Maher, K. & Pallansch, M. A. ( 2004c; ). Complete genome sequences of all members of the species Human enterovirus A. J Gen Virol 85, 1597–1607.[CrossRef]
    [Google Scholar]
  29. Oberste, M. S., Peñaranda, S. & Pallansch, M. A. ( 2004d; ). RNA recombination plays a major role in genomic change during circulation of coxsackie B viruses. J Virol 78, 2948–2955.[CrossRef]
    [Google Scholar]
  30. Oprisan, G., Combiescu, M., Guillot, S., Caro, V., Combiescu, A., Delpeyroux, F. & Crainic, R. ( 2002; ). Natural genetic recombination between co-circulating heterotypic enteroviruses. J Gen Virol 83, 2193–2200.
    [Google Scholar]
  31. Paananen, A., Ylipaasto, P., Rieder, E., Hovi, T., Galama, J. & Roivainen, M. ( 2003; ). Molecular and biological analysis of echovirus 9 strain isolated from a diabetic child. J Med Virol 69, 529–537.[CrossRef]
    [Google Scholar]
  32. Pallansch, M. A. & Roos, R. P. ( 2001; ). Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses. In Fields Virology, 4th edn, pp. 723–775. Edited by D. M. Knipe & P. M. Howley. Philadelphia, PA: Lippincott Williams & Wilkins
  33. Robertson, D. L., Hahn, B. H. & Sharp, P. M. ( 1995; ). Recombination in AIDS viruses. J Mol Evol 40, 249–259.[CrossRef]
    [Google Scholar]
  34. Salminen, M. O., Carr, J. K., Burke, D. S. & McCutchan, F. E. ( 1995; ). Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 11, 1423–1425.[CrossRef]
    [Google Scholar]
  35. Santti, J., Hyypiä, T., Kinnunen, L. & Salminen, M. ( 1999; ). Evidence of recombination among enteroviruses. J Virol 73, 8741–8749.
    [Google Scholar]
  36. Santti, J., Harvala, H., Kinnunen, L. & Hyypiä, T. ( 2000; ). Molecular epidemiology and evolution of coxsackievirus A9. J Gen Virol 81, 1361–1372.
    [Google Scholar]
  37. Sawyer, S. A. ( 1989; ). Statistical tests for detecting gene conversion. Mol Biol Evol 6, 526–538.
    [Google Scholar]
  38. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
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