1887

Journal of General Virology header logo

Volume 88, Issue 11

Full-length genome sequences of hepatitis C virus subtype 4f Free

Abstract

Hepatitis C virus genotype 4 (HCV-4) is very common in central Africa, prevalent in the Middle East, and is becoming increasingly frequent among southern Europeans. We have determined the complete nucleotide sequences of HCV-4f strains and investigated their phylogenetic relationships with other genotypes. We amplified the complete genome of two HCV subtype 4f strains, IFBT84 and IFBT88. The HCV-4f strains have a total of 9181 and 9304 nt, respectively, including the 5′ untranslated region followed by a single open reading frame. There was no evidence of genomic recombination in the IFBT84 and IFBT88 strains. The sequences of the HCV-4f strain genomes are closer to those of HCV-1b than to genotypes 2, 3, 5 and 6. It is important to know the full-length sequences of HCV-4 subtypes in order to classify them correctly and to obtain more detailed knowledge about HCV epidemiology and sensitivity to interferon.

  • Received:
  • Accepted:
  • Published Online:
SGM
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83151-0
2007-11-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/jgv/88/11/2985.html?itemId=/content/journal/jgv/10.1099/vir.0.83151-0&mimeType=html&fmt=ahah

References

  1. Basso M., Torre F., Grasso A., Percario G., Azzola E., Artioli S., Blanchi S., Pelli N., Picciotto A. 2007; Pegylated interferon and ribavirin in re-treatment of responder-relapser HCV patients. Dig Liver Dis 39:47–51 [CrossRef]
     [Google Scholar]
  2. Cenci M., Massi M., Alderisio M., De Soccio G., Recchia O. 2007; Prevalence of hepatitis C virus (HCV) genotypes and increase of type 4 in central Italy: an update and report of a new method of HCV genotyping. Anticancer Res 27:1219–1222
     [Google Scholar]
  3. Chamberlain R. W., Adams N., Saeed A. A., Simmonds P., Elliott R. M. 1997; Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J Gen Virol 78:1341–1347
     [Google Scholar]
  4. Derbala M., Am A., Bener A., Lopez A. C., Omar M., El Ghannam M. 2005; Pegylated interferon-alpha 2b-ribavirin combination in Egyptian patients with genotype 4 chronic hepatitis. J Viral Hepat 12:380–385 [CrossRef]
     [Google Scholar]
  5. Franco S., Tural C., Clotet B., Martinez M. A. 2007; Complete nucleotide sequence of genotype 4 hepatitis C viruses isolated from patients co-infected with human immunodeficiency virus type 1. Virus Res 123:161–169 [CrossRef]
     [Google Scholar]
  6. Fretz C., Jeannel D., Stuyver L., Herve V., Lunel F., Boudifa A., Mathiot C., de The G., Fournel J. J. 1995; HCV infection in a rural population of the Central African Republic (CAR): evidence for three additional subtypes of genotype 4. J Med Virol 47:435–437 [CrossRef]
     [Google Scholar]
  7. Fried M. W., Shiffman M. L., Reddy K. R., Smith C., Marinos G., Goncales F. L. Jr, Haussinger D., Diago M., Carosi G. other authors 2002; Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Engl J Med 347:975–982 [CrossRef]
     [Google Scholar]
  8. Genovese D., Dettori S., Argentini C., Villano U., Chionne P., Angelico M., Rapicetta M. 2005; Molecular epidemiology of hepatitis C virus genotype 4 isolates in Egypt and analysis of the variability of envelope proteins E1 and E2 in patients with chronic hepatitis. J Clin Microbiol 43:1902–1909 [CrossRef]
     [Google Scholar]
  9. Hasan F., Asker H., Al-Khaldi J., Siddique I., Al-Ajmi M., Owaid S., Varghese R., Al-Nakib B. 2004; Peginterferon alfa-2b plus ribavirin for the treatment of chronic hepatitis C genotype 4. Am J Gastroenterol 99:1733–1737 [CrossRef]
     [Google Scholar]
  10. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150–163 [CrossRef]
     [Google Scholar]
  11. Lauer G. M., Walker B. D. 2001; Hepatitis C virus infection. N Engl J Med 345:41–52 [CrossRef]
     [Google Scholar]
  12. Legrand-Abravanel F., Nicot F., Boulestin A., Sandres-Saune K., Vinel J. P., Alric L., Izopet J. 2005; Pegylated interferon and ribavirin therapy for chronic hepatitis C virus genotype 4 infection. J Med Virol 77:66–69 [CrossRef]
     [Google Scholar]
  13. Manns M. P., McHutchison J. G., Gordon S. C., Rustgi V. K., Shiffman M., Reindollar R., Goodman Z. D., Koury K., Ling M., Albrecht J. K. 2001; Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial. Lancet 358:958–965 [CrossRef]
     [Google Scholar]
  14. Martin D. P., Williamson C., Posada D. 2005; RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262 [CrossRef]
     [Google Scholar]
  15. Mellor J., Holmes E. C., Jarvis L. M., Yap P. L., Simmonds P. 1995; Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. The International HCV Collaborative Study Group. J Gen Virol 76:2493–2507 [CrossRef]
     [Google Scholar]
  16. Miller M. J., Powell J. I. 1994; A quantitative comparison of DNA sequence assembly programs. J Comput Biol 1:257–269 [CrossRef]
     [Google Scholar]
  17. Morice Y., Roulot D., Grando V., Stirnemann J., Gault E., Jeantils V., Bentata M., Jarrousse B., Lortholary O. other authors 2001; Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns. J Gen Virol 82:1001–1012
     [Google Scholar]
  18. Nguyen M. H., Keeffe E. B. 2005; Prevalence and treatment of hepatitis C virus genotypes 4, 5, and 6. Clin Gastroenterol Hepatol 3:S97–S101 [CrossRef]
     [Google Scholar]
  19. Nicot F., Legrand-Abravanel F., Sandres-Saune K., Boulestin A., Dubois M., Alric L., Vinel J. P., Pasquier C., Izopet J. 2005; Heterogeneity of hepatitis C virus genotype 4 strains circulating in south-western France. J Gen Virol 86:107–114 [CrossRef]
     [Google Scholar]
  20. Njouom R., Pasquier C., Ayouba A., Gessain A., Froment A., Mfoupouendoun J., Pouillot R., Dubois M., Sandres-Saune K. other authors 2003; High rate of hepatitis C virus infection and predominance of genotype 4 among elderly inhabitants of a remote village of the rain forest of South Cameroon. J Med Virol 71:219–225 [CrossRef]
     [Google Scholar]
  21. Page R. D. M. 1996; TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
     [Google Scholar]
  22. Pasquier C., Njouom R., Ayouba A., Dubois M., Sartre M. T., Vessiere A., Timba I., Thonnon J., Izopet J., Nerrienet E. 2005; Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon. J Med Virol 77:390–398 [CrossRef]
     [Google Scholar]
  23. Ray S. C., Arthur R. R., Carella A., Bukh J., Thomas D. L. 2000; Genetic epidemiology of hepatitis C virus throughout Egypt. J Infect Dis 182:698–707 [CrossRef]
     [Google Scholar]
  24. Ray Kim W. 2002; Global epidemiology and burden of hepatitis C. Microbes Infect 4:1219–1225 [CrossRef]
     [Google Scholar]
  25. Robertson B., Myers G., Howard C., Brettin T., Bukh J., Gaschen B., Gojobori T., Maertens G., Mizokami M. other authors 1998; Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch Virol 143:2493–2503 [CrossRef]
     [Google Scholar]
  26. Salemi M., Vandamme A. M. 2002; Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences. J Mol Evol 54:62–70 [CrossRef]
     [Google Scholar]
  27. Sandres-Saune K., Deny P., Pasquier C., Thibaut V., Duverlie G., Izopet J. 2003; Determining hepatitis C genotype by analyzing the sequence of the NS5b region. J Virol Methods 109:187–193 [CrossRef]
     [Google Scholar]
  28. Schroter M., Feucht H. H., Zollner B., Schafer P., Laufs R. 2003; Multiple infections with different HCV genotypes: prevalence and clinical impact. J Clin Virol 27:200–204 [CrossRef]
     [Google Scholar]
  29. Sharara A. I., Ramia S., Ramlawi F., Fares J. E., Klayme S., Naman R. 2007; Genotypes of hepatitis C virus (HCV) among positive Lebanese patients: comparison of data with that from other Middle Eastern countries. Epidemiol Infect 135:427–432 [CrossRef]
     [Google Scholar]
  30. Simmonds P., Bukh J., Combet C., Deleage G., Enomoto N., Feinstone S., Halfon P., Inchauspe G., Kuiken C. other authors 2005; Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962–973 [CrossRef]
     [Google Scholar]
  31. 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]
  32. Timm J., Neukamm M., Kuntzen T., Kim A. Y., Chung R. T., Brander C., Lauer G. M., Walker B. D., Allen T. M. 2007; Characterization of full-length hepatitis C virus genotype 4 sequences. J Viral Hepat 14:330–337 [CrossRef]
     [Google Scholar]
  33. van Asten L., Verhaest I., Lamzira S., Hernandez-Aguado I., Zangerle R., Boufassa F., Rezza G., Broers B., Robertson J. R. other authors 2004; Spread of hepatitis C virus among European injection drug users infected with HIV: a phylogenetic analysis. J Infect Dis 189:292–302 [CrossRef]
     [Google Scholar]
  34. Wohnsland A., Hofmann W. P., Sarrazin C. 2007; Viral determinants of resistance to treatment in patients with hepatitis C. Clin Microbiol Rev 20:23–38 [CrossRef]
     [Google Scholar]
  35. Xu L. Z., Larzul D., Delaporte E., Brechot C., Kremsdorf D. 1994; Hepatitis C virus genotype 4 is highly prevalent in central Africa (Gabon). J Gen Virol 75:2393–2398 [CrossRef]
     [Google Scholar]
  36. Zeuzem S., Hultcrantz R., Bourliere M., Goeser T., Marcellin P., Sanchez-Tapias J., Sarrazin C., Harvey J., Brass C., Albrecht J. 2004; Peginterferon alfa-2b plus ribavirin for treatment of chronic hepatitis C in previously untreated patients infected with HCV genotypes 2 or 3. J Hepatol 40:993–999 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.83151-0
Loading
Full-length genome sequences of hepatitis C virus subtype 4f
J. Gen. Virol. 88, 2985 (2007); https://doi.org/10.1099/vir.0.83151-0
/content/journal/jgv/10.1099/vir.0.83151-0
/content/journal/jgv/10.1099/vir.0.83151-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error