Sequences reported in this study have been submitted in Genbank. Their accession numbers are: EU408330–32.
Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u†
Article first published online: 19 AUG 2008
Copyright © 2008 Wiley-Liss, Inc.
Journal of Medical Virology
Volume 80, Issue 10, pages 1740–1746, October 2008
How to Cite
Xia, X., Zhao, W., Tee, K. K., Feng, Y., Takebe, Y., Li, Q., Pybus, O. G. and Lu, L. (2008), Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u. J. Med. Virol., 80: 1740–1746. doi: 10.1002/jmv.21287
- Issue published online: 21 AUG 2008
- Article first published online: 19 AUG 2008
- Manuscript Accepted: 1 JUL 2008
- Natural Science Foundation of China (NSFC; partial support). Grant Number: 30460119
- International Collaboration Project. Grant Number: 2006GH07
- Natural Science and Application Project (Yunnan Provincial Government, China). Grant Number: 2007C038M
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. J. Med. Virol. 80:1740–1746, 2008. © 2008 Wiley-Liss, Inc.