1887

Abstract

(CCHF) has attracted considerable attention recently and a number of phylogenetic studies have been published, based mostly on partial sequences of S and M RNA segments. In this study, available full-length S, M and L segment sequences of CCHF virus were checked for recombination. Similarity plots and bootscan analysis of the S segment suggested multiple recombination events between southern European, Asian and African CCHF virus strains, with additional evidence provided by phylogenetic trees, the hidden Markov model and probabilistic divergence measures methods. No unambiguous signs of recombination were observed for M and L segments; however, the results did not exclude the possibility of this. These findings, coupled with a recent report on reassortment in CCHF virus, suggest caution when assessing CCHF virus phylogeny based on short sequence fragments.

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2005-08-01
2024-04-19
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References

  1. Bridgen A., Dalrymple D. A., Elliott R. M. 2002; Dugbe nairovirus S segment: correction of published sequence and comparison of five isolates. Virology 294:364–371 [CrossRef]
    [Google Scholar]
  2. Chare E. R., Gould E. A., Holmes E. C. 2003; Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 84:2691–2703 [CrossRef]
    [Google Scholar]
  3. Chinikar S., Persson S. M., Johansson M. 7 other authors 2004; Genetic analysis of Crimean-congo hemorrhagic fever virus in Iran. J Med Virol 73:404–411 [CrossRef]
    [Google Scholar]
  4. Chumakov M. P., Butenko A. M., Shalunova N. V. 10 other authors 1968; New data on the viral agent of Crimean hemorrhagic fever (in Russian). Vopr Virusol 13:377
    [Google Scholar]
  5. Elliott R. M., Bouloy M., Calisher C. H., Goldbach R., Moyer J. T., Nichol S. T., Pettersson R., Plyusnin A., Schmaljohn C. S. 2000; Family Bunyaviridae . In Virus Taxonomy. Seventh Report International Committee for the Taxonomy of Viruses pp  599–621 Edited by van Regenmortel M. H. V., Fauquet C. M., Bishop D. H. L., Carstens E. B., Estes M. K., Lemon S., Maniloff J., Mayo M. A., McGeogh D., Pringle C. R., Wickner R. B. San Diego: Academic Press;
    [Google Scholar]
  6. Felsenstein J. 1989; phylip - Phylogeny Inference Package (Version 3.2). Cladistics 5:164–166
    [Google Scholar]
  7. Hewson R., Gmyl A., Gmyl L., Smirnova S. E., Karganova G., Jamil B., Hasan R., Chamberlain J., Clegg C. 2004; Evidence of segment reassortment in Crimean-Congo haemorrhagic fever virus. J Gen Virol 85:3059–3070 [CrossRef]
    [Google Scholar]
  8. Honig J. E., Osborne J. C., Nichol S. T. 2004; Crimean-Congo hemorrhagic fever virus genome L RNA segment and encoded protein. Virology 321:29–35 [CrossRef]
    [Google Scholar]
  9. Hoogstraal H. 1979; The epidemiology of tick-borne Crimean-Congo hemorrhagic fever in Asia, Europe, and Africa. J Med Entomol 15:307–417 [CrossRef]
    [Google Scholar]
  10. Husmeier D., Wright F. 2001; Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17:S123–S131 [CrossRef]
    [Google Scholar]
  11. Husmeier D., McGuire G. 2003; Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo. Mol Biol Evol 20:315–337 [CrossRef]
    [Google Scholar]
  12. Kinsella E., Martin S. G., Grolla A., Czub M., Feldmann H., Flick R. 2004; Sequence determination of the Crimean-Congo hemorrhagic fever virus L segment. Virology 321:23–28 [CrossRef]
    [Google Scholar]
  13. Marriott A. C., Nuttall P. A. 1992; Comparison of the S RNA segments and nucleoprotein sequences of Crimean-Congo hemorrhagic fever, Hazara, and Dugbe viruses. Virology 189:795–799 [CrossRef]
    [Google Scholar]
  14. Marriott A. C., Polyzoni T., Antoniadis A., Nuttall P. A. 1994; Detection of human antibodies to Crimean-Congo haemorrhagic fever virus using expressed viral nucleocapsid protein. J Gen Virol 75:2157–2161 [CrossRef]
    [Google Scholar]
  15. 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]
  16. Morikawa S., Qing T., Xinqin Z., Saijo M., Kurane I. 2002; Genetic diversity of the M RNA segment among Crimean-Congo hemorrhagic fever virus isolates in China. Virology 296:159–164 [CrossRef]
    [Google Scholar]
  17. Nichol S. T. 2001; Bunyaviruses. In Fields Virology . , 4th edn. pp  1603–1634 Edited by Knipe D. M., Howley P. M. Philadelphia: Lippincott Williams & Wilkins;
  18. Nichol S. T., Arikawa J., Kawaoka Y. 2000; Emerging viral diseases. Proc Natl Acad Sci U S A 97:12411–12412 [CrossRef]
    [Google Scholar]
  19. Papa A., Ma B., Kouidou S., Tang Q., Hang C., Antoniadis A. 2002a; Genetic characterization of the M RNA segment of Crimean Congo hemorrhagic fever virus strains, China. Emerg Infect Dis 8:50–53 [CrossRef]
    [Google Scholar]
  20. Papa A., Bozovi B., Pavlidou V., Papadimitriou E., Pelemis M., Antoniadis A. 2002b; Genetic detection and isolation of Crimean-Congo hemorrhagic fever virus , Kosovo, Yugoslavia. Emerg Infect Dis 8:852–854 [CrossRef]
    [Google Scholar]
  21. Papa A., Bino S., Llagami A. 9 other authors 2002c; Crimean-Congo hemorrhagic fever in Albania, 2001. Eur J Clin Microbiol Infect Dis 21:603–606 [CrossRef]
    [Google Scholar]
  22. Petrova I. D., Seregin S. V., Petrov V. S. 8 other authors 2003; Genetic characteristics of the S-segment of RNA from two strains of the Crimean-Congo hemorrhagic fever virus isolated in the south of Russia and in Uzbekistan (in Russian). Vopr Virusol 48:8–11
    [Google Scholar]
  23. Ray S. C. 1999 SimPlot for Windows 95/98/NT, 2.5 edn. Distributed by the author http://sray.med.som.jhmi.edu/RaySoft/SimPlot/
    [Google Scholar]
  24. Rodriguez L. L., Maupin G. O., Ksiazek T. G. 8 other authors 1997; Molecular investigation of a multisource outbreak of Crimean-Congo hemorrhagic fever in the United Arab Emirates. Am J Trop Med Hyg 57:512–518
    [Google Scholar]
  25. 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]
  26. Sanchez A. J., Vincent M. J., Nichol S. T. 2002; Characterization of the glycoproteins of Crimean-Congo hemorrhagic fever virus. J Virol 76:7263–7275 [CrossRef]
    [Google Scholar]
  27. Schmaljohn C. S., Hooper J. W. 2001; Bunyaviridae : the viruses and their replication. In Fields Virology , 4th edn. pp  1447–1472 Edited by Knipe D. M., Howley P. M. Philadelphia: Lippincott Williams & Wilkins;
    [Google Scholar]
  28. Seregin S. V., Samokhvalov E. I., Petrova I. D. 8 other authors 2004; Genetic characterization of the M RNA segment of Crimean-Congo hemorrhagic fever virus strains isolated in Russia and Tajikistan. Virus Genes 28:187–193 [CrossRef]
    [Google Scholar]
  29. Shepherd A. J., Swanepoel R., Gill D. E. 1988; Evaluation of enzyme-linked immunosorbent assay and reversed passive hemagglutination for detection of Crimean-Congo hemorrhagic fever virus antigen. J Clin Microbiol 26:347–353
    [Google Scholar]
  30. Sibold C., Meisel H., Kruger D. H., Labuda M., Lysy J., Kozuch O., Pejcoch M., Vaheri A., Plyusnin A. 1999; Recombination in Tula hantavirus evolution: analysis of genetic lineages from Slovakia. J Virol 73:667–675
    [Google Scholar]
  31. 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]
  32. Yashina L., Vyshemirskii O., Seregin S. 9 other authors 2003a; Genetic analysis of Crimean-Congo hemorrhagic fever virus in Russia. J Clin Microbiol 41:860–862 [CrossRef]
    [Google Scholar]
  33. Yashina L., Petrova I., Seregin S. 10 other authors 2003b; Genetic variability of Crimean-Congo haemorrhagic fever virus in Russia and Central Asia. J Gen Virol 84:1199–1206 [CrossRef]
    [Google Scholar]
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