Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t

J Gen Virol. 2009 Aug;90(Pt 8):1820-1826. doi: 10.1099/vir.0.010330-0. Epub 2009 Apr 8.

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'.

MeSH terms

  • Adult
  • Aged
  • Canada
  • Cluster Analysis
  • Emigrants and Immigrants
  • Female
  • Genome, Viral*
  • Genotype
  • Hepacivirus / genetics*
  • Hepacivirus / isolation & purification
  • Hepatitis C / virology
  • Humans
  • Male
  • Middle Aged
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Viral / genetics*
  • Sequence Analysis, DNA*
  • Sequence Homology, Nucleic Acid
  • Serum / virology

Substances

  • RNA, Viral

Associated data

  • GENBANK/FJ462431
  • GENBANK/FJ462432
  • GENBANK/FJ462433
  • GENBANK/FJ462434
  • GENBANK/FJ462435
  • GENBANK/FJ462436
  • GENBANK/FJ462437
  • GENBANK/FJ462438
  • GENBANK/FJ462439
  • GENBANK/FJ462440
  • GENBANK/FJ462441
  • GENBANK/FJ839869
  • GENBANK/FJ839870