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Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6

¹ Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
² The First People’s Hospital of Yunnan Province, Kunming, China
³ Gunagzhou Blood Center, Guangzhou City, Guangdong Province, China
⁴ Public Health Laboratories, New Hampshire Department of Health and Human Services, Concord, NH, USA
⁵ Department of Zoology, Oxford University, Oxford, UK
⁶ Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
⁷ Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken, Japan
⁸ Institut National de Santé Publique du Quebec, Laboratoire de Santé Publique du Quebec, Sainte-Anne-de-Bellevue, Quebec, Canada

Correspondence
Ling Lu
llu{at}kumc.edu
Donald Murphy
Donald.Murphy{at}inspq.qc.ca

Five hepatitis C virus (HCV) complete genome sequences (Th846, 537796, QC227, QC216 and QC99) from a blood donor in Thailand and three Asian immigrants and one Caucasian in North America were determined. Phylogenetically, they represent the first complete genomes for subtypes 6c, 6l, 6o, 6p and 6q, respectively. Similarity analysis showed no evidence of inter- or intrasubtype recombination. Further analysis in conjunction with partial sequences from the Los Alamos HCV database led to the identification of other closely related isolates from south-eastern Asia or immigrants from that region. However, Th846 did not cluster with any reference sequence and is the sole isolate of subtype 6c reported so far. This study completes the full genome sequencing of all 17 assigned HCV genotype 6 subtypes (6a–6q). The utility of this panel of complete sequences for accurate detection and classification of infection, and for estimating the origin of this genotype of HCV, is discussed.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this study are EF424625–EF424629.

A table showing pairwise nucleotide similarities of the five HCV complete genomic sequences with other genotype 6 subtypes and a diagram outlining the strategy used to amplify the five complete HCV genomic sequences are available as supplementary material in JGV Online.

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