1887

Abstract

Accurate viral genotyping is important. Here I investigate genotypes in hepatitis E virus (HEV) and find that the open reading frame (ORF) structure (the lengths of three ORFs and the overlapping relationships among the ORFs) can be a good criterion for genotyping HEV. An inter-genotype recombinant (GenBank accession no. DQ450072) was revealed by analysing the ORF structure and confirmed by phylogenetic analyses. This discovery of the inter-genotype recombinant indicates that genotyping in HEV should be based on full-length sequences. The Mexican strain which is currently classified as a genotype 2 strain also exhibited the mosaic sequence pattern, although without statistical support.

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2009-06-01
2024-04-19
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References

  1. Anderson J. P., Rodrigo A. G., Learn G. H., Madan A., Delahunty C., Coon M., Girard M., Osmanov S., Hood L., Mullins J. I. 2000; Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. J Virol 74:10752–10765 [CrossRef]
    [Google Scholar]
  2. Arankalle V. A., Paranjape S., Emerson S. U., Purcell R. H., Walimbe A. M. 1999; Phylogenetic analysis of hepatitis E virus isolates from India (1976–1993). J Gen Virol 80:1691–1700
    [Google Scholar]
  3. Aye T. T., Uchida T., Ma X. Z., Iida F., Shikata T., Zhuang H., Win K. M. 1992; Complete nucleotide sequence of a hepatitis E virus isolated from the Xinjiang epidemic (1986–1988) of China. Nucleic Acids Res 20:3512 [CrossRef]
    [Google Scholar]
  4. Bradley D. W. 1990a; Enterically-transmitted non-A, non-B hepatitis. Br Med Bull 46:442–461
    [Google Scholar]
  5. Bradley D. W. 1990b; Hepatitis non-A, non-B viruses become identified as hepatitis C and E viruses. Prog Med Virol 37:101–135
    [Google Scholar]
  6. Bryan J. P., Tsarev S. A., Iqbal M., Ticehurst J., Emerson S., Ahmed A., Duncan J., Rafiqui A. R. other authors 1994; Epidemic hepatitis E in Pakistan: patterns of serologic response and evidence that antibody to hepatitis E virus protects against disease. J Infect Dis 170:517–521 [CrossRef]
    [Google Scholar]
  7. Buisson Y., Grandadam M., Nicand E., Cheval P., van Cuyck-Gandre H., Innis B., Rehel P., Coursaget P., Teyssou R., Tsarev S. 2000; Identification of a novel hepatitis E virus in Nigeria. J Gen Virol 81:903–909
    [Google Scholar]
  8. Chatterjee R., Tsarev S., Pillot J., Coursaget P., Emerson S. U., Purcell R. H. 1997; African strains of hepatitis E virus that are distinct from Asian strains. J Med Virol 53:139–144 [CrossRef]
    [Google Scholar]
  9. Coursaget P., Buisson Y., N'Gawara M. N., Van Cuyck-Gandre H., Roue R. 1998; Role of hepatitis E virus in sporadic cases of acute and fulminant hepatitis in an endemic area (Chad). Am J Trop Med Hyg 58:330–334
    [Google Scholar]
  10. Cubitt D., Bradley D. W., Carter M. J., Chiba S., Estes M. K., Saif L. J., Schaffer F. L., Smith A. W., Studdert M. J., Thiel H. J. 1995; Family Caliciviridae . In Virus Taxonomy: Classification and Nomenclature of Viruses: Sixth Report of the International Committee on Taxonomy of Viruses [for the] Virology Division, International Union of Microbiological Societies pp 359–363Edited by Murphy F. A., Fauquet C. M., Bishop D. H. L., Ghabrial S. A., Jarvis A. W., Martelli G. P., Mayo M. A., Summers M. D. Wien, New York: Springer-Verlag;
    [Google Scholar]
  11. Emerson S. U., Purcell R. H. 2003; Hepatitis E virus. Rev Med Virol 13:145–154 [CrossRef]
    [Google Scholar]
  12. Emerson S. U., Anderson D., Arankalle A., Meng X. J., Purdy M., Schlauder G. G., Tsarev S. A. 2005; Hepevirus. In Virus Taxonomy: Classification and Nomenclature of Viruses: Eighth Report of the International Committee on the Taxonomy of Viruses pp 853–857Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball. London; San Diego, CA: Elsevier/Academic Press;
    [Google Scholar]
  13. Erker J. C., Desai S. M., Schlauder G. G., Dawson G. J., Mushahwar I. K. 1999; A hepatitis E virus variant from the United States: molecular characterization and transmission in cynomolgus macaques. J Gen Virol 80:681–690
    [Google Scholar]
  14. Feinstone S. M., Purcell R. H. 1978; Non-A, non-B hepatitis. Annu Rev Med 29:359–366 [CrossRef]
    [Google Scholar]
  15. Gouvea V., Hoke C. H., Innis B. L. 1998; Genotyping of hepatitis E virus in clinical specimens by restriction endonuclease analysis. J Virol Methods 70:71–78 [CrossRef]
    [Google Scholar]
  16. Hsieh S. Y., Yang P. Y., Ho Y. P., Chu C. M., Liaw Y. F. 1998; Identification of a novel strain of hepatitis E virus responsible for sporadic acute hepatitis in Taiwan. J Med Virol 55:300–304 [CrossRef]
    [Google Scholar]
  17. Huang C.-C., Nguyen D., Fernandez J., Yun K. Y., Fry K. E., Bradley D. W., Tam A. W., Reyes G. R. 1992; Molecular cloning and sequencing of the Mexico isolate of hepatitis E virus (HEV). Virology 191:550–558 [CrossRef]
    [Google Scholar]
  18. Koonin E. V., Gorbalenya A. E., Purdy M. A., Rozanov M. N., Reyes G. R., Bradley D. W. 1992; Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of an positive-strand RNA plant and animal viruses. Proc Natl Acad Sci U S A 89:8259–8263 [CrossRef]
    [Google Scholar]
  19. Maydt J., Lengauer T. 2006; Recco: recombination analysis using cost optimization. Bioinformatics 22:1064–1071 [CrossRef]
    [Google Scholar]
  20. Meng X. J., Halbur P. G., Haynes J. S., Tsareva T. S., Bruna J. D., Royer R. L., Purcell R. H., Emerson S. U. 1998; Experimental infection of pigs with the newly identified swine hepatitis E virus (swine HEV), but not with human strains of HEV. Arch Virol 143:1405–1415 [CrossRef]
    [Google Scholar]
  21. Posada D., Crandall K. A. 1998; modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
    [Google Scholar]
  22. Schlauder G. G., Mushahwar I. K. 2001; Genetic heterogeneity of hepatitis E virus. J Med Virol 65:282–292 [CrossRef]
    [Google Scholar]
  23. Schlauder G. G., Dawson G. J., Erker J. C., Kwo P. Y., Knigge M. F., Smalley D. L., Rosenblatt J. E., Desai S. M., Mushahwar I. K. 1998; The sequence and phylogenetic analysis of a novel hepatitis E virus isolated from a patient with acute hepatitis reported in the United States. J Gen Virol 79:447–456
    [Google Scholar]
  24. Schlauder G. G., Desai S. M., Zanetti A. R., Tassopoulos N. C., Mushahwar I. K. 1999; Novel hepatitis E virus (HEV) isolates from Europe: evidence for additional genotypes of HEV. J Med Virol 57:243–251 [CrossRef]
    [Google Scholar]
  25. Shrestha M. P., Scott R. M., Joshi D. M., Mammen M. P. Jr, Thapa G. B., Thapa N., Myint K. S., Fourneau M., Kuschner R. A. other authors 2007; Safety and efficacy of a recombinant hepatitis E vaccine. N Engl J Med 356:895–903 [CrossRef]
    [Google Scholar]
  26. Swofford D. 1999 paup* phylogenetic analysis using parsimony (*and other methods Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  27. Takahashi M., Nishizawa T., Yoshikawa A., Sato S., Isoda N., Ido K., Sugano K., Okamoto H. 2002; Identification of two distinct genotypes of hepatitis E virus in a Japanese patient with acute hepatitis who had not travelled abroad. J Gen Virol 83:1931–1940
    [Google Scholar]
  28. Tam A. W., Smith M. M., Guerra M. E., Huang C.-C., Bradley D. W., Fry K. E., Reyes G. R. 1991; Hepatitis E virus (HEV): molecular cloning and sequencing of the full-length viral genome. Virology 185:120–131 [CrossRef]
    [Google Scholar]
  29. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  30. Wang Y., Ling R., Erker J. C., Zhang H., Li H., Desai S., Mushahwar I. K., Harrison T. J. 1999; A divergent genotype of hepatitis E virus in Chinese patients with acute hepatitis. J Gen Virol 80:169–177
    [Google Scholar]
  31. Wang Y., Zhang H., Ling R., Li H., Harrison T. J. 2000; The complete sequence of hepatitis E virus genotype 4 reveals an alternative strategy for translation of open reading frames 2 and 3. J Gen Virol 81:1675–1686
    [Google Scholar]
  32. Worm H. C., van der Poel W. H. M., Brandstatter G. 2002; Hepatitis E: an overview. Microbes Infect 4:657–666 [CrossRef]
    [Google Scholar]
  33. Yang Z., Wong W. S. W., Nielsen R. 2005; Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118 [CrossRef]
    [Google Scholar]
  34. Zanetti A. R., Schlauder G. G., Romano L., Tanzi E., Fabris P., Dawson G. J., Mushahwar I. K. 1999; Identification of a novel variant of hepatitis E virus in Italy. J Med Virol 57:356–360 [CrossRef]
    [Google Scholar]
  35. Zhai L., Dai X., Meng J. 2006; Hepatitis E virus genotyping based on full-length genome and partial genomic regions. Virus Res 120:57–69 [CrossRef]
    [Google Scholar]
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