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A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3

Division of Gastroenterology and Hepatology, University Hospital, 24 rue Micheli-du-Crest, 1211 Geneva, Switzerland¹
Swiss Institute of Bioinformatics² and Division of Clinical Pathology³, CMU, 1 rue Michel-Servet, 1211 Geneva, Switzerland

Author for correspondence: Francesco Negro (at University Hospital). Fax +41 22 3729366. e-mail Francesco.Negro{at}dim.hcuge.ch

Hepatitis C virus (HCV) sequences from throughout the world have been grouped into six clades, based on recently proposed criteria. Here, the partial sequences and clade assignment are reported for three HCV isolates from chronic hepatitis C patients from Somalia, for whom conventional assays failed to identify the genotype. Phylogenetic analysis of the sequences of the core, envelope 1 and part of the non- structural 5b regions suggests that all three isolates belong to a distinct HCV genetic group, tentatively classified as subtype 3h. This novel HCV subtype shows the highest sequence similarity with HCV isolates from Indonesia. Despite the fact that these patients were infected with HCV clade 3, none of them responded to standard interferon treatment.

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