1887

Abstract

In this study, we characterized the full-length genomic sequences of 13 distinct hepatitis C virus (HCV) genotype 4 isolates/subtypes: QC264/4b, QC381/4c, QC382/4d, QC193/4g, QC383/4k, QC274/4l, QC249/4m, QC97/4n, QC93/4o, QC139/4p, QC262/4q, QC384/4r and QC155/4t. These were amplified, using RT-PCR, from the sera of patients now residing in Canada, 11 of which were African immigrants. The resulting genomes varied between 9421 and 9475 nt in length and each contains a single ORF of 9018–9069 nt. The sequences showed nucleotide similarities of 77.3–84.3 % in comparison with subtypes 4a (GenBank accession no. Y11604) and 4f (EF589160) and 70.6–72.8 % in comparison with genotype 1 (M62321/1a, M58335/1b, D14853/1c, and 1?/AJ851228) reference sequences. These similarities were often higher than those currently defined by HCV classification criteria for subtype (75.0–80.0 %) and genotype (67.0–70.0 %) division, respectively. Further analyses of the complete and partial E1 and partial NS5B sequences confirmed these 13 ‘provisionally assigned subtypes’.

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2009-08-01
2021-01-20
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References

  1. Angelico M., Renganathan E., Gandin C., Fathy M., Profili M. C., Refai W., De Santis A., Nagi A., Amin G. other authors 1997; Chronic liver disease in the Alexandria governorate, Egypt: contribution of schistosomiasis and hepatitis virus infections. J Hepatol 26:236–243 [CrossRef]
    [Google Scholar]
  2. Ansaldi F., Bruzzone B., Salmaso S., Rota M. C., Durando P., Gasparini R., Icardi G. 2005; Different seroprevalence and molecular epidemiology patterns of hepatitis C virus infection in Italy. J Med Virol 76:327–332 [CrossRef]
    [Google Scholar]
  3. Bukh J., Purcell R. H., Miller R. H. 1992; Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc Natl Acad Sci U S A 89:4942–4946 [CrossRef]
    [Google Scholar]
  4. 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]
  5. Colina R., Casane D., Vasquez S., Garcia-Aguirre L., Chunga A., Romero H., Khan B., Cristina J. 2004; Evidence of intratypic recombination in natural populations of hepatitis C virus. J Gen Virol 85:31–37 [CrossRef]
    [Google Scholar]
  6. Fernández-Arcás N., López-Siles J., Trapero S., Ferraro A., Ibáñez A., Orihuela F., Maldonado J., Alonso A. 2006; High prevalence of hepatitis C virus subtypes 4c and 4d in Malaga (Spain): phylogenetic and epidemiological analyses. J Med Virol 78:1429–1435 [CrossRef]
    [Google Scholar]
  7. Franco S., Tural C., Clotet B., Martínez 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]
  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. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [CrossRef]
    [Google Scholar]
  10. Hmaied F., Legrand-Abravanel F., Nicot F., Garrigues N., Chapuy-Regaud S., Dubois M., Njouom R., Izopet J., Pasquier C. 2007; Full-length genome sequences of hepatitis C virus subtype 4f. J Gen Virol 88:2985–2990 [CrossRef]
    [Google Scholar]
  11. 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 [CrossRef]
    [Google Scholar]
  12. Kalinina O., Norder H., Magnius L. O. 2004; Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formation. J Gen Virol 85:1853–1857 [CrossRef]
    [Google Scholar]
  13. Kamal S. M., Nasser I. A. 2008; Hepatitis C genotype 4: what we know and what we don't yet know. Hepatology 47:1371–1383 [CrossRef]
    [Google Scholar]
  14. Katsoulidou A., Sypsa V., Tassopoulos N. C., Boletis J., Karafoulidou A., Ketikoglou I., Tsantoulas D., Vafiadi I., Hatzis G. other authors 2006; Molecular epidemiology of hepatitis C virus (HCV) in Greece: temporal trends in HCV genotype-specific incidence and molecular characterization of genotype 4 isolates. J Viral Hepat 13:19–27 [CrossRef]
    [Google Scholar]
  15. 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]
  16. Kuntzen T., Berical A., Ndjomou J., Bennett P., Schneidewind A., Lennon N., Birren B. W., Kuiken C., Henn M. R. other authors 2008; A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame. J Med Virol 80:1370–1378 [CrossRef]
    [Google Scholar]
  17. Kwok S., Higuchi R. 1989; Avoiding false positives with PCR. Nature 339:237–238 [CrossRef]
    [Google Scholar]
  18. Legrand-Abravanel F., Claudinon J., Nicot F., Dubois M., Chapuy-Regaud S., Sandres-Saune K., Pasquier C., Izopet J. 2007; New natural intergenotypic (2/5) recombinant of hepatitis C virus. J Virol 81:4357–4362 [CrossRef]
    [Google Scholar]
  19. Li C., Fu Y., Lu L., Ji W., Yu J., Hagedorn C. H., Zhang L. 2006; Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection. J Med Virol 78:1061–1069 [CrossRef]
    [Google Scholar]
  20. Lu L., Li C., Fu Y., Thaikruea L., Thongswat S., Maneekarn N., Apichartpiyakul C., Hotta H., Okamoto H. other authors 2007; Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses. J Gen Virol 88:1505–1518 [CrossRef]
    [Google Scholar]
  21. Lyra A. C., Ramrakhiani S., Bacon B. R., Di Bisceglie A. M. 2004; Infection with hepatitis C virus genotype 4 in the United States. J Clin Gastroenterol 38:68–71 [CrossRef]
    [Google Scholar]
  22. Martin D. P., Williamson C., Posada D. 2005; rdp2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262 [CrossRef]
    [Google Scholar]
  23. 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]
  24. Murphy D. G., Willems B., Deschênes M., Hilzenrat N., Mousseau R., Sabbah S. 2007; Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5′ untranslated region sequences. J Clin Microbiol 45:1102–1112 [CrossRef]
    [Google Scholar]
  25. Ndjomou J., Pybus O. G., Matz B. 2003; Phylogenetic analysis of hepatitis C virus isolates indicates a unique pattern of endemic infection in Cameroon. J Gen Virol 84:2333–2341 [CrossRef]
    [Google Scholar]
  26. Ndong-Atome G. R., Makuwa M., Ouwe-Missi-Oukem-Boyer O., Pybus O. G., Branger M., Le Hello S., Boye-Cheik S. B., Brun-Vezinet F., Kazanji M. other authors 2008; High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural Gabon. J Med Virol 80:1581–1587 [CrossRef]
    [Google Scholar]
  27. 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]
  28. Njouom R., Pasquier C., Ayouba A., Gessain A., Froment A., Mfoupouendoun J., Pouillot R., Dubois M., Sandres-Sauné 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]
  29. Njouom R., Pasquier C., Ayouba A., Tejiokem M. C., Vessiere A., Mfoupouendoun J., Tene G., Eteki N., Lobe M. M. other authors 2005; Low risk of mother-to-child transmission of hepatitis C virus in Yaounde, Cameroon: the ANRS 1262 study. Am J Trop Med Hyg 73:460–466
    [Google Scholar]
  30. Njouom R., Nerrienet E., Dubois M., Lachenal G., Rousset D., Vessière A., Ayouba A., Pasquier C., Pouillot R. 2007; The hepatitis C virus epidemic in Cameroon: genetic evidence for rapid transmission between 1920 and 1960. Infect Genet Evol 7:361–367 [CrossRef]
    [Google Scholar]
  31. Noppornpanth S., Lien T. X., Poovorawan Y., Smits S. L., Osterhaus A. D., Haagmans B. L. 2006; Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus. J Virol 80:7569–7577 [CrossRef]
    [Google Scholar]
  32. Pasquier C., Njouom R., Ayouba A., Dubois M., Sartre M. T., Vessière A., Timba I., Thonnon J., Izopet J. other authors 2005; Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon. J Med Virol 77:390–398 [CrossRef]
    [Google Scholar]
  33. Payan C., Roudot-Thoraval F., Marcellin P., Bled N., Duverlie G., Fouchard-Hubert I., Trimoulet P., Couzigou P., Cointe D. other authors 2005; Changing of hepatitis C virus genotype patterns in France at the beginning of the third millennium: the GEMHEP GenoCII Study. J Viral Hepat 12:405–413 [CrossRef]
    [Google Scholar]
  34. Posada D., Crandall K. A. 1998; modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
    [Google Scholar]
  35. Pybus O. G., Drummond A. J., Nakano T., Robertson B. H., Rambaut A. 2003; The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol Biol Evol 20:381–387 [CrossRef]
    [Google Scholar]
  36. 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]
  37. 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]
  38. Simmonds P. 2004; Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85:3173–3188 [CrossRef]
    [Google Scholar]
  39. 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]
  40. Smith D. B., Pathirana S., Davidson F., Lawlor E., Power J., Yap P. L., Simmonds P. 1997; The origin of hepatitis C virus genotypes. J Gen Virol 78:321–328
    [Google Scholar]
  41. Stuyver L., van Arnhem W., Wyseur A., Hernandez F., Delaporte E., Maertens G. 1994; Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes. Proc Natl Acad Sci U S A 91:10134–10138 [CrossRef]
    [Google Scholar]
  42. Tanaka Y., Agha S., Saudy N., Kurbanov F., Orito E., Kato T., Abo-Zeid M., Khalaf M., Miyakawa Y. other authors 2004; Exponential spread of hepatitis C virus genotype 4a in Egypt. J Mol Evol 58:191–195 [CrossRef]
    [Google Scholar]
  43. 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]
  44. Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Miyakawa Y., Mayumi M. 1998; The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7–9 and comparison with those in the other eight genetic groups. J Gen Virol 79:1847–1857
    [Google Scholar]
  45. van Doorn L. J., Kleter B., Stuyver L., Maertens G., Brouwer H., Schalm S., Heijtink R., Quint W. 1994; Analysis of hepatitis C virus genotypes by a line probe assay and correlation with antibody profiles. J Hepatol 21:122–129 [CrossRef]
    [Google Scholar]
  46. Xu L. Z., Larzul D., Delaporte E., Bréchot 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]
  47. Zein N. N., Rakela J., Krawitt E. L., Reddy K. R., Tominaga T., Persing D. H. 1996; Hepatitis C virus genotypes in the United States: epidemiology, pathogenicity, and response to interferon therapy. Collaborative Study Group. Ann Intern Med 125:634–639 [CrossRef]
    [Google Scholar]
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