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Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6

Ling Lu^1,

Chunhua Li^1,3,

¹ Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
² Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
³ The First People's Hospital of Yunnan Province, Kunming, PR China
⁴ Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, PR China
⁵ Department of Immunology and Physiopathology, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam
⁶ Department of Microbiology, Hebei Medical University, Shijiazhuang, PR China
⁷ Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan

Correspondence
Ling Lu
ling.lu{at}hsc.utah.edu
Kenji Abe
kenjiabe{at}nih.go.jp

In this study, the complete genomic sequence was determined for three hepatitis C virus variants (VT21, TV241 and TV249) of genotype 6 that do not classify within the established subtypes. All three genomes were isolated from patients in Vietnam and sequenced using 100 µl of serum. They showed 91.4–93.6 % nucleotide similarities to each other but only 71.7–79.4 % similarities to 17 reference sequences representing subtypes 6a–6q and to isolates km41 and gz52557. VT21, TV241 and TV249 displayed genome lengths of 9407, 9460 and 9445 nt, respectively. All three isolates contained a single open reading frame of 9051 nt while the 5'UTRs and 3'UTRs were 324–338 nt and 32–71 nt, respectively. They shared common sizes with QC227/6o and QC216/6p isolates in all ten protein regions. Phylogenetic analyses demonstrated that VT21, TV241 and TV249 clustered independently and were assigned subtype 6t, following the recent designations of 6r and 6s. Analysis of partial genomic sequences available for genotype 6 variants revealed five additional subtype 6t isolates, all originating from Vietnam. This analysis revealed two additional groups of isolates, and at least seven novel variants analogous to km41 and gz52557 that group independently and do not classify within the subtypes 6a–6t. This suggests the existence of at least 11 additional subtypes for genotype 6. In addition, the existence of isolates showing genetic distances greater than those within subtypes, but lesser than those between subtypes, raises interesting questions regarding the classification of HCV.

These authors contributed equally to this paper.

The GenBank/EMBL/DDBJ sequence accession numbers for the sequences reported in this study are EF632069–632071.

A supplementary table showing the primers used in this study is available with the online version of this paper.