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Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t

¹ Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
² Department of Biology, Kunming Teacher's College, Kunming, Yunnan, PR China
³ Guangzhou Blood Center, Guangzhou, Guangdong, PR China
⁴ Micropathology Ltd, University of Warwick Science Park, Coventry, UK
⁵ University of Georgia, Athens, GA, USA
⁶ Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada

Correspondence
Ling Lu
ling.lu{at}hsc.utah.edu
Donald Murphy
donald.murphy{at}inspq.qc.ca

In this study, we characterized the full-length genomic sequences of 13 distinct hepatitis C virus (HCV) genotype 4 isolates/subtypes: QC264/4b, QC381/4c, QC382/4d, QC193/4g, QC383/4k, QC274/4l, QC249/4m, QC97/4n, QC93/4o, QC139/4p, QC262/4q, QC384/4r and QC155/4t. These were amplified, using RT-PCR, from the sera of patients now residing in Canada, 11 of which were African immigrants. The resulting genomes varied between 9421 and 9475 nt in length and each contains a single ORF of 9018–9069 nt. The sequences showed nucleotide similarities of 77.3–84.3 % in comparison with subtypes 4a (GenBank accession no. Y11604) and 4f (EF589160 [GenBank] ) and 70.6–72.8 % in comparison with genotype 1 (M62321/1a, M58335/1b, D14853/1c, and 1?/AJ851228) reference sequences. These similarities were often higher than those currently defined by HCV classification criteria for subtype (75.0–80.0 %) and genotype (67.0–70.0 %) division, respectively. Further analyses of the complete and partial E1 and partial NS5B sequences confirmed these 13 ‘provisionally assigned subtypes’.

The GenBank/EMBL/DDBJ accession number for sequences reported are FJ462431 (QC139/4p), FJ462432 (QC193/4g), FJ462433 (QC249/4m), FJ462434 (QC262/4q), FJ462435 (QC264/4b), FJ462436 (QC381/4c), FJ462437 (QC382/4d), FJ462438 (QC383/4k), FJ462439 (QC384/4r), FJ462440 (QC93/4o), FJ462441 (QC97/4n), FJ839869 (QC155/4t) and FJ839870 (QC274/4l).

Supplementary tables are available with the online version of this paper.