1887

Abstract

Analysis of partial hepatitis C virus sequences has revealed many novel genotype 6 variants that cannot be unambiguously classified, which obscure the distinctiveness of pre-existing subtypes. To explore this uncertainty, we obtained genomes of 98.0–98.8 % full-length for eight such variants (KM35, QC273, TV257, TV476, TV533, L349, QC271 and DH027) and characterized them using phylogenetic analyses and per cent nucleotide similarities. The former four are closely related phylogenetically to subtype 6k, TV533 and L349 to subtype 6l, QC271 to subtypes 6i and 6j, and DH027 to subtypes 6m and 6n. The former six defined a high-level grouping that comprised subtypes 6k and 6l, plus related strains. The threshold between intra- and inter-subtype diversity in this group was indistinct. We propose that similar results would be seen elsewhere if more intermediate variants like QC271 and DH027 were sampled.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.047506-0
2013-01-01
2019-12-14
Loading full text...

Full text loading...

/deliver/fulltext/jgv/94/1/76.html?itemId=/content/journal/jgv/10.1099/vir.0.047506-0&mimeType=html&fmt=ahah

References

  1. 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.[PubMed]
    [Google Scholar]
  2. Fu Y., Wang Y., Xia W., Pybus O. G., Qin W., Lu L., Nelson K.. ( 2011;). New trends of HCV infection in China revealed by genetic analysis of viral sequences determined from first-time volunteer blood donors. . J Viral Hepat 18:, 42–52. [CrossRef][PubMed]
    [Google Scholar]
  3. Guindon S., Gascuel O.. ( 2003;). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52:, 696–704. [CrossRef][PubMed]
    [Google Scholar]
  4. Kuiken C., Yusim K., Boykin L., Richardson R.. ( 2005;). The Los Alamos hepatitis C sequence database. . Bioinformatics 21:, 379–384. [CrossRef][PubMed]
    [Google Scholar]
  5. Kumar S., Tamura K., Nei M.. ( 2004;). mega3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. . Brief Bioinform 5:, 150–163. [CrossRef][PubMed]
    [Google Scholar]
  6. Kwok S., Higuchi R.. ( 1989;). Avoiding false positives with PCR. . Nature 339:, 237–238. [CrossRef][PubMed]
    [Google Scholar]
  7. 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][PubMed]
    [Google Scholar]
  8. 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][PubMed]
    [Google Scholar]
  9. 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][PubMed]
    [Google Scholar]
  10. Martin D. P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P.. ( 2010;). rdp3: a flexible and fast computer program for analyzing recombination. . Bioinformatics 26:, 2462–2463. [CrossRef][PubMed]
    [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.[PubMed]
    [Google Scholar]
  12. 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][PubMed]
    [Google Scholar]
  13. Noppornpanth S., Sablon E., De Nys K., Lien T. X., Brouwer J., Van Brussel M., Smits S. L., Poovorawan Y., Osterhaus A. D. M. E., 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][PubMed]
    [Google Scholar]
  14. Pham V. H., Nguyen H. D., Ho P. T., Banh D. V., Pham H. L., Pham P. H., Lu L., Abe K.. ( 2011;). Very high prevalence of hepatitis C virus genotype 6 variants in southern Vietnam: large-scale survey based on sequence determination. . Jpn J Infect Dis 64:, 537–539.[PubMed]
    [Google Scholar]
  15. Pybus O. G., Barnes E., Taggart R., Lemey P., Markov P. V., Rasachak B., Syhavong B., Phetsouvanah R., Sheridan I.. & other authors ( 2009;). Genetic history of hepatitis C virus in East Asia. . J Virol 83:, 1071–1082. [CrossRef][PubMed]
    [Google Scholar]
  16. Rambaut A., Robertson D. L., Pybus O. G., Peeters M., Holmes E. C.. ( 2001;). Human immunodeficiency virus. Phylogeny and the origin of HIV-1. . Nature 410:, 1047–1048. [CrossRef][PubMed]
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. 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.[PubMed]
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. Simmonds P., Bukh J., Combet C., Deléage G., Enomoto N., Feinstone S., Halfon P., Inchauspé G., Kuiken C.. & other authors ( 2005;). Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. . Hepatology 42:, 962–973. [CrossRef][PubMed]
    [Google Scholar]
  21. Stuyver L., Wyseur A., van Arnhem W., Lunel F., Laurent-Puig P., Pawlotsky J. M., Kleter B., Bassit L., Nkengasong J.. & 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][PubMed]
    [Google Scholar]
  22. Syhavong B., Rasachack B., Smythe L., Rolain J. M., Roque-Afonso A. M., Jenjaroen K., Soukkhaserm V., Phongmany S., Phetsouvanh R.. & other authors ( 2010;). The infective causes of hepatitis and jaundice amongst hospitalised patients in Vientiane, Laos. . Trans R Soc Trop Med Hyg 104:, 475–483. [CrossRef][PubMed]
    [Google Scholar]
  23. 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][PubMed]
    [Google Scholar]
  24. 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.[PubMed]
    [Google Scholar]
  25. Tippmann H. F.. ( 2004;). Analysis for free: comparing programs for sequence analysis. . Brief Bioinform 5:, 82–87. [CrossRef][PubMed]
    [Google Scholar]
  26. Vidal N., Peeters M., Mulanga-Kabeya C., Nzilambi N., Robertson D., Ilunga W., Sema H., Tshimanga K., Bongo B., Delaporte E.. ( 2000;). Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. . J Virol 74:, 10498–10507. [CrossRef][PubMed]
    [Google Scholar]
  27. Xia X., Lu L., Tee K. K., Zhao W., Wu J., Yu J., Li X., Lin Y., Mukhtar M. M.. & other authors ( 2008;). The unique HCV genotype distribution and the discovery of a novel subtype 6u among IDUs co-infected with HIV-1 in Yunnan, China. . J Med Virol 80:, 1142–1152. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.047506-0
Loading
/content/journal/jgv/10.1099/vir.0.047506-0
Loading

Data & Media loading...

Supplements

Supplementary tables 

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