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Full length genome sequences were characterized for three novel hepatitis C virus (HCV) isolates (here named DH012, DH014, and DH028). The complete genomes were all isolated from injecting drug users (IDUs) who were co-infected with HIV-1 and lived in Dehong prefecture, Yunnan Province, China, which neighbors Myanmar. The three genomes are 9,443-9,470 nt in length and each contains a single open reading frame (ORF) of 9,069 nt long. Pairwise comparisons indicated nucleotide similarities of 97.9-98.6% among the three isolates, and similarities of 72.4-75.0% between the three isolates and 20 reference strains (representing HCV subtypes 6a-6q and 6t plus two unassigned genotype 6 isolates km41 and gz52557). Phylogenetic analyses demostrated that the three isolates formed a tight and well-supported monophyletic cluster in the genotype 6 clade. No evidence of viral recombination was found using similarity plots and bootscanning analyses. Based on the current HCV classification criteria, we have assigned the three isolates to a new subtype, 6u. Although another "6u" isolate D83 has been reported very recently, it is subtypically distinct from the three isolates we described here. Because its designation does not meet the criteria described in the updated HCV nomenclature proposal, this "6u" isolate should be reclassified.

Original publication

DOI

10.1002/jmv.21287

Type

Journal article

Journal

J Med Virol

Publication Date

10/2008

Volume

80

Pages

1740 - 1746

Keywords

Adult, Base Sequence, China, Genetic Variation, Genome, Viral, HIV Infections, HIV-1, Hepacivirus, Hepatitis C, Humans, Male, Molecular Sequence Data, Phylogeny, Recombination, Genetic, Sequence Analysis, RNA, Sequence Homology, Substance Abuse, Intravenous