1887

Abstract

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5′ untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3′ UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81400-0
2006-03-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/jgv/87/3/629.html?itemId=/content/journal/jgv/10.1099/vir.0.81400-0&mimeType=html&fmt=ahah

References

  1. Apichartpiyakul C., Chittivudikarn C., Miyajima H., Homma M., Hotta H. 1994; Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai. Thailand. J Clin Microbiol 32:2276–2279
    [Google Scholar]
  2. Bernier L., Willems B., Delage G., Murphy D. G. 1996; Identification of numerous hepatitis C virus genotypes in Montreal, Canada. J Clin Microbiol 34:2815–2818
    [Google Scholar]
  3. Doi H., Apichartpiyakul C., Ohba K., Mizokami M., Hotta H. 1996; Hepatitis C virus (HCV) subtype prevalence in Chiang Mai, Thailand, and identification of novel subtypes of HCV major type 6. J Clin Microbiol 34:569–574
    [Google Scholar]
  4. 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]
  5. Inoue Y., Sulaiman H. A., Matsubayashi K., Julitasari I. K., Ansari A., Laras K., Corwin A. L. 2000; Genotypic analysis of hepatitis C virus in blood donors in Indonesia. Am J Trop Med Hyg 62:92–98
    [Google Scholar]
  6. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
    [Google Scholar]
  7. 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]
  8. Lu L., Nakano T., He Y., Fu Y., Hagedorn C. H., Robertson B. H. 2005a; Hepatitis C virus genotype distribution in China: predominance of closely related subtype 1b isolates and existence of new genotype 6 variants. J Med Virol 75:538–549 [CrossRef]
    [Google Scholar]
  9. Lu L., Nakano T., Smallwood G. A., Heffron T. G., Robertson B. H., Hagedorn C. H. 2005b; A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: application to a novel hepatitis C virus variant of genotype 6. J Virol Methods 126:139–148 [CrossRef]
    [Google Scholar]
  10. 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]
  11. Mellor J., Walsh E. A., Prescott L. E., Jarvis L. M., Davidson F., Yap P. L., Simmonds P. 1996; Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay. J Clin Microbiol 34:417–423
    [Google Scholar]
  12. Robertson B., Myers G., Howard C. & 14 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]
  13. Shinji T., Kyaw Y. Y., Gokan K. & 13 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]
  14. Simmonds P., Alberti A., Alter H. J. & 43 other authors 1994; A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321–1324 [CrossRef]
    [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 77:3013–3024 [CrossRef]
    [Google Scholar]
  16. Simmonds P., Bukh J., Combet C. & 19 other authors 2005; Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962–973 [CrossRef]
    [Google Scholar]
  17. Stuyver L., Wyseur A., van Arnhem W. & 8 other authors 1995; Hepatitis C virus genotyping by means of 5′-UR/core line probe assays and molecular analysis of untypeable samples. Virus Res 38:137–157 [CrossRef]
    [Google Scholar]
  18. Thaikruea L., Thongsawat S., Maneekarn N., Netski D., Thomas D. L., Nelson K. E. 2004; Risk factors for hepatitis C virus infection among blood donors in northern Thailand. Transfusion 44:1433–1440 [CrossRef]
    [Google Scholar]
  19. Theamboonlers A., Chinchai T., Bedi K., Jantarasamee P., Sripontong M., Poovorawan Y. 2002; Molecular characterization of hepatitis C virus (HCV) core region in HCV-infected Thai blood donors. Acta Virol 46:169–173
    [Google Scholar]
  20. Tokita H., Okamoto H., Tsuda F. & 7 other authors 1994; Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc Natl Acad Sci U S A 91:11022–11026 [CrossRef]
    [Google Scholar]
  21. 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]
  22. Zhang L., Chen Z., Cao Y. & 14 other authors 2004; Molecular characterization of human immunodeficiency virus type 1 and hepatitis C virus in paid blood donors and injection drug users in china. J Virol 78:13591–13599 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81400-0
Loading
/content/journal/jgv/10.1099/vir.0.81400-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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