1887

Abstract

Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (5′UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 5′UTR–core sequences found strain PE22 to be related to subtype 1b. However, the same analysis using the NS5B region found it to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection.

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2004-01-01
2020-11-27
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References

  1. Alter H. J., Seeff L. B. 2000; Recovery, persistence, and sequelae in hepatitis C virus infection: a perspective on long-term outcome. Sem Liver Dis 20:17–35
    [Google Scholar]
  2. Becher P., Orlich M., Thiel H.-J. 2001; RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease. J Virol 75:6256–6264
    [Google Scholar]
  3. Blok J., McWilliam S. M., Butler H. C. 7 other authors 1992; Comparison of a dengue-2 virus and its candidate vaccine derivative: sequence relationships with the flaviviruses and other viruses. Virology 187:573–590
    [Google Scholar]
  4. Chan S. W., McOmish F., Holmes E. C., Dow B., Peutherer J. F., Follett E., Yap P. L., Simmonds P. 1992; Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. J Gen Virol 73:1131–1141
    [Google Scholar]
  5. Chen W.-R., Tesh R. B., Rico-Hesse R. 1990; Genetic variation of Japanese encephalitis virus in nature. J Gen Virol 71:2915–2922
    [Google Scholar]
  6. Colina R., Azambuja C., Uriarte R., Mogdasy C., Cristina J. 1999; Evidence of increasing diversification of hepatitis C viruses. J Gen Virol 80:1377–1382
    [Google Scholar]
  7. Costa-Mattioli M., Ferre V., Casane D. 7 other authors 2003; Evidence of recombination in natural populations of hepatitis A virus. Virology 311:51–59
    [Google Scholar]
  8. Cristina J., Mukomolov S., Colina R., Kalinina O., García L., Khan B., Mogdasy C., Karayiannis P. 2002; Hepatitis C virus phylogeny: a useful clinical tool. Acta Virol 46:179–182
    [Google Scholar]
  9. Dixit V., Quan S., Martin P. 7 other authors 1995; Evaluation of a novel serotyping system for hepatitis C virus: strong correlation with standard genotyping methodologies. J Clin Microbiol 33:2978–2983
    [Google Scholar]
  10. Domingo E., Holland J. J. 1997; RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151–178
    [Google Scholar]
  11. Felsenstein J. 1993 Phylogeny interference package, version 3.5 Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  12. Georgescu M. M., Delpeyroux F., Tardypanit 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]
  13. 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
    [Google Scholar]
  14. Holmes E. C., Worobey M., Rambaut A. 1999; Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16:405–409
    [Google Scholar]
  15. Kalinina O., Norder H., Mukomolov S., Magnius L. O. 2002; A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 76:4034–4043
    [Google Scholar]
  16. Kew O. M., Nottay B. K. 1984; Evolution of the oral polio vaccine strains in humans occurs by both mutation and intramolecular recombination. In Modern Approaches to Vaccines pp  357–363 Edited by Chanock R. M., Lerner R. A. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  17. Kew O., Morris-Glasgow V., Landaverde M. 21 other authors 2002; Outbreak of poliomyelitis in Hispaniola associated with circulating type 1 vaccine-derived poliovirus. Science 296:356–359
    [Google Scholar]
  18. Kumar S., Tamura K., Nei M. 1994; mega: Molecular Evolutionary Genetic Analysis software for microcomputers. Comput Appl Biosci 10:189–191
    [Google Scholar]
  19. Kuno G. 1997; Factors influencing the transmission of dengue viruses. In Dengue and Dengue Haemorrhagic Fever Edited by Gubler D. J., Kuno G. Wallingford, UK: CAB International;
    [Google Scholar]
  20. Kwok S., Higuchi R. 1989; Avoiding false positives with PCR. Nature 339:237–238
    [Google Scholar]
  21. Leitmeyer K. C., Vaughn D. W., Watts D. M., Salas R., Villalobos de Chacon I., Ramos C., Rico-Hesse R. 1999; Dengue virus structural differences that correlate with pathogenesis. J Virol 73:4738–4747
    [Google Scholar]
  22. Lole K. S., Bollinger R. C., Paranjape R. S., Gadkari D., Kulkarni S. S., Novak N. G., Ingersoll R., Sheppard H. W., Ray S. C. 1999; Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160
    [Google Scholar]
  23. Martin J., Samoilovich E., Dunn G. 7 other authors 2002; Isolation of an intertypic poliovirus capsid recombinant from a child with vaccine-associated paralytic poliomyelitis. J Virol 76:10921–10928
    [Google Scholar]
  24. Monath T. P. 1994; Dengue: the risk to developed and developing countries. Proc Natl Acad Sci U S A 91:2395–2400
    [Google Scholar]
  25. Muller H. J. 1964; The relation of recombination to mutational advance. Mut Res 1:2–9
    [Google Scholar]
  26. Najera R., Delgado E., Perez-Alvarez L., Thomson M. M. 2002; Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 16:S3–S16
    [Google Scholar]
  27. Norder H., Bergström A., Uhnoo I., Alden J., Weiss L., Czajkowski J., Magnius L. 1998; Confirmation of nosocomial transmission of hepatitis C virus by phylogenetic analysis of the NS5B region. J Clin Microbiol 36:3066–3069
    [Google Scholar]
  28. Ohno O., Mizokami M., Wu R. R., Saleh M. G., Ohba K. I., Orito E., Mukaide M., Williams R., Lau J. Y. N. 1997; New hepatitis C virus (HCV) genotyping system that allows for identification of HCV genotypes 1a, 1b, 2a, 2b, 3a, 3b, 4, 5a and 6a. J Clin Microbiol 35:201–207
    [Google Scholar]
  29. Okamoto H., Tokita H., Sakamoto M., Horikita M., Kojima M., Iizuka H., Mishiro S. 1993; Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and primers for specific detection. J Gen Virol 74:2385–2390
    [Google Scholar]
  30. Onafuwa A., An W., Robson N. D., Telesnitsky A. 2003; Human immunodeficiency virus type 1 genetic recombination is more frequent than that of Moloney murine leukemia virus despite similar template switching rates. J Virol 77:4577–4587
    [Google Scholar]
  31. Prescott L. E., Berger A., Pawlotsky J. M., Conjeevaram P., Pike I., Simmonds P. 1997; Sequence analysis of hepatitis C virus variants producing discrepant results with two different genotyping assays. J Med Virol 53:237–244
    [Google Scholar]
  32. Rambaut A., Grassly N. C. 1997; Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp Appl Biosci 13:235–238
    [Google Scholar]
  33. Rico-Hesse R. 1990; Molecular evolution and distribution of dengue viruses type 1 and 2 in nature. Virology 174:479–493
    [Google Scholar]
  34. San Roman M., Lezama L., Rojas E., Colina R., García L., Carlos A., Khan B., Cristina J. 2002; Analysis of genetic heterogeneity of hepatitis C viruses in Central America reveals a novel genetic lineage. Arch Virol 147:2239–2246
    [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. Simmonds P. 1999; Viral heterogeneity of the hepatitis C virus. J Hepatol 31:54–60
    [Google Scholar]
  37. Simmonds P., Rose K. A., Graham S., Chan S. W., McOmish F., Dow B. C., Follett E. A. C., Yap P. L., Marsden H. 1993; Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV): use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3. J Clin Microbiol 31:1493–1503
    [Google Scholar]
  38. Simmonds P., Smith D. B., McOmish F., Yap P. L., Kolberg J., Urdea M. S., Holmes E. C. 1994; Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. J Gen Virol 75:1053–1061
    [Google Scholar]
  39. Smith D. B., Simmonds P. 1997; Molecular epidemiology of hepatitis C virus. J Gastroenterol Hepatol 12:522–527
    [Google Scholar]
  40. Strimmer K., Forslund K., Holland B., Moulton V. 2003; A novel exploratory method for visual recombination detection. Genome Biol 4:R33
    [Google Scholar]
  41. Stuyver L., Rossau R., Wyseur A., Duhamel M., Venderborght B., van Heuverswyn H., Maertens G. 1993; Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J Gen Virol 74:1093–1102
    [Google Scholar]
  42. Stuyver L., Wyseur A., van Arnhem W. 8 other authors 1995; Hepatitis C virus genotyping by means of 5′-UR/core line probe assay and molecular analysis of untypeable samples. Virus Res 38:137–157
    [Google Scholar]
  43. Suzuki Y., Gojobori T., Nakagomi O. 1998; Intragenic recombinations in rotaviruses. FEBS Lett 427:183–187
    [Google Scholar]
  44. 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
    [Google Scholar]
  45. Tolou H., Couissinier-Paris P., Durand J. P., Mercier V., de Pina J. J., de Micco P., Billoir F., Charrel R. N., de Lamballerie X. 2001; Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J Gen Virol 82:1283–1290
    [Google Scholar]
  46. Twiddy S. S., Holmes E. C. 2003; The extent of homologous recombination in members of the genus Flavivirus . J Gen Virol 84:429–440
    [Google Scholar]
  47. Uzcategui N. Y., Camacho D., Comach G., Cuello de Uzcategui R., Holmes E. C., Gould E. A. 2001; The molecular epidemiology of dengue type 2 virus in Venezuela: evidence for in situ virus evolution and recombination. J Gen Virol 82:2945–2953
    [Google Scholar]
  48. Vega I., Colina R., García L., Uriarte R., Mogdasy C., Cristina J. 2001; Diversification of hepatitis C viruses in South America reveals a novel genetic lineage. Arch Virol 146:1623–1629
    [Google Scholar]
  49. Viazov S., Widell A., Nordenfelt E. 2000; Mixed infection with two types of hepatitis C virus is probably a rare event. Infection 28:21–25
    [Google Scholar]
  50. Vidal N., Koyalta D., Richard V., Lechiche C., Ndinaromtan T., Djimasngar A., Delaporte E., Peeters M. 2003; High genetic diversity of HIV-1 strains in Chad, West Central Africa. J Acquir Immune Defic Syndr 33:239–246
    [Google Scholar]
  51. Worobey M., Holmes E. C. 1999; Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80:2535–2543
    [Google Scholar]
  52. Worobey M., Holmes E. C. 2001; Homologous recombination in GB virus C/hepatitis G virus. Mol Biol Evol 18:254–261
    [Google Scholar]
  53. Worobey M., Rambaut A., Holmes E. C. 1999; Widespread intra-serotype recombination in natural populations of dengue virus. Proc Natl Acad Sci U S A 96:7352–7357
    [Google Scholar]
  54. Yagani M., St Claire M., Shapiro M., Emerson S. U., Purcell H., Bukh J. 1998; Transcripts of a chimeric cDNA clone of hepatitis C virus genotype 1b are infectious in vivo. Virology 244:161–172
    [Google Scholar]
  55. Yun Z., Lara C., Johansson B., Lorenzana de Rivera I., Sönnerborg A. 1996; Discrepancy of hepatitis C virus genotypes as determined by phylogenetic analysis of partial NS5 and core sequences. J Med Virol 49:155–160
    [Google Scholar]
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