Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6

• Published in: Journal of general virology 2006-03, Vol.87 (3), p.629-634
• Main Authors: Lu, Ling, Nakano, Tatsunori, Li, Chunhua, Fu, Yongshui, Miller, Steve, Kuiken, Carla, Robertson, Betty H, Hagedorn, Curt H
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; China; Fundamental and applied biological sciences. Psychology; Genome, Viral; Hepacivirus - classification; Hepacivirus - genetics; Hepatitis C - virology; Hepatitis C virus; Humans; Microbiology; Miscellaneous; Molecular Sequence Data; Species Specificity; Virology
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/vir.0.81400-0

1 Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA 2 Department of Internal Medicine, Ichinomiya Nishi Hospital, Ichinomiya, Aichi, Japan 3 Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China 4 Graduate School of the Chinese Academy of Sciences, Beijing, China 5 Guangzhou Blood Center, Guangzhou City, Guangdong Province, China 6 Los Alamos National Laboratory, Los Alamos, NM, USA 7 National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA Correspondence Ling Lu llu{at}kumc.edu 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. The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are DQ278892–DQ278894. Supplementary material is available in JGV Online. Deceased 21 November 2005; this paper has been dedicated to her memory by her former research fellows Ling Lu and Tatsunori Nakano. These authors contributed equally to this work.