1887

Abstract

In this study, the complete genomic sequence was determined for three hepatitis C virus variants (VT21, TV241 and TV249) of genotype 6 that do not classify within the established subtypes. All three genomes were isolated from patients in Vietnam and sequenced using 100 μl of serum. They showed 91.4–93.6 % nucleotide similarities to each other but only 71.7–79.4 % similarities to 17 reference sequences representing subtypes 6a–6q and to isolates km41 and gz52557. VT21, TV241 and TV249 displayed genome lengths of 9407, 9460 and 9445 nt, respectively. All three isolates contained a single open reading frame of 9051 nt while the 5′UTRs and 3′UTRs were 324–338 nt and 32–71 nt, respectively. They shared common sizes with QC227/6o and QC216/6p isolates in all ten protein regions. Phylogenetic analyses demonstrated that VT21, TV241 and TV249 clustered independently and were assigned subtype 6t, following the recent designations of 6r and 6s. Analysis of partial genomic sequences available for genotype 6 variants revealed five additional subtype 6t isolates, all originating from Vietnam. This analysis revealed two additional groups of isolates, and at least seven novel variants analogous to km41 and gz52557 that group independently and do not classify within the subtypes 6a–6t. This suggests the existence of at least 11 additional subtypes for genotype 6. In addition, the existence of isolates showing genetic distances greater than those within subtypes, but lesser than those between subtypes, raises interesting questions regarding the classification of HCV.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83460-0
2008-02-01
2019-11-12
Loading full text...

Full text loading...

/deliver/fulltext/jgv/89/2/444.html?itemId=/content/journal/jgv/10.1099/vir.0.83460-0&mimeType=html&fmt=ahah

References

  1. 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]
  2. Hoofnagle, J. H. ( 2002; ). Course and outcome of hepatitis C. Hepatology 36, S21–S29.
    [Google Scholar]
  3. 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]
  4. 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]
  5. Lu, L., Nakano, T., Li, C., Fu, Y., Miller, S., Kuiken, C., Robertson, B. H. & Hagedorn, C. H. ( 2006; ). Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J Gen Virol 87, 629–634.[CrossRef]
    [Google Scholar]
  6. Lu, L., Li, C., Fu, Y., Thaikruea, L., Thongswat, S., Maneekarn, N., Apichartpiyakul, C., Hotta, H., Okamoto, H. & other authors ( 2007a; ). 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]
  7. Lu, L., Li, C., Fu, Y., Gao, F., Pybus, O. G., Abe, K., Okamoto, H., Hagedorn, C. H. & Murphy, D. ( 2007b; ). Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6. J Gen Virol 88, 1519–1525.[CrossRef]
    [Google Scholar]
  8. Lwin, A. A., Shinji, T., Khin, M., Win, N., Obika, M., Okada, S. & Koide, N. ( 2007; ). Hepatitis C virus genotype distribution in Myanmar: predominance of genotype 6 and existence of new genotype 6 subtype. Hepatol Res 37, 337–345.[CrossRef]
    [Google Scholar]
  9. Major, M. E. & Feinstone, S. M. ( 1997; ). The molecular virology of hepatitis C. Hepatology 25, 1527–1538.[CrossRef]
    [Google Scholar]
  10. Martin, D. P., Williamson, C. & Posada, D. ( 2005; ). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260–262.[CrossRef]
    [Google Scholar]
  11. 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]
  12. Noppornpanth, S., Sablon, E., Nys, K. D., Truong, X. L., Brouwer, J., van Brussel, M., Smits, S. L., Poovorawan, Y., Osterhaus, A. D. & Haagmans, B. L. ( 2006; ). Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5′ untranslated regions. J Clin Microbiol 44, 3969–3974.[CrossRef]
    [Google Scholar]
  13. 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]
  14. Shinji, T., Kyaw, Y. Y., Gokan, K., Tanaka, Y., Ochi, K., Kusano, N., Mizushima, T., Fujioka, S., Shiraha, H. & other authors ( 2004; ). Analysis of HCV genotypes from blood donors shows three new HCV type 6 subgroups exist in Myanmar. Acta Med Okayama 58, 135–142.
    [Google Scholar]
  15. Simmonds, P., Mellor, J., Sakuldamrongpanich, T., Nuchaprayoon, C., Tanprasert, S., Holmes, E. C. & Smith, D. B. ( 1996; ). Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity. J Gen Virol 77, 3013–3014.[CrossRef]
    [Google Scholar]
  16. 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]
  17. World Health Organization ( 1999; ). Hepatitis C global prevalence. Wkly Epidemiol Rec 74, 425–427.
    [Google Scholar]
  18. Zoulim, F., Chevallier, M., Maynard, M. & Trepo, C. ( 2003; ). Clinical consequences of hepatitis C virus infection. Rev Med Virol 13, 57–68.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.83460-0
Loading
/content/journal/jgv/10.1099/vir.0.83460-0
Loading

Data & Media loading...

Supplements

vol. , part 2, pp. 444–452

PCR primers and amplification strategy [PDF](184 KB)



PDF

Most Cited This Month

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