Hepatitis C virus sequences from different patients confirm the existence and transmissibility of subtype 2q, a rare subtype circulating in the metropolitan area of Barcelona, Spain

Authors

  • Elisa Martró,

    Corresponding author
    1. Microbiology Service, Health Sciences Research Institute of the “Germans Trias i Pujol” Foundation, “Germans Trias i Pujol” Hospital, Autonoma University of Barcelona, Badalona, Spain
    2. Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Barcelona, Spain
    • Microbiology Service, Hospital Universitari Germans Trias i Pujol, Ctra. del Canyet s/n, 08916 Badalona, Spain.
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  • Ana Valero,

    1. Centre for Infectious Diseases, Microbial Pathogenesis Unit, University of Edinburgh, Edinburgh, United Kingdom
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  • Elena Jordana-Lluch,

    1. Microbiology Service, Health Sciences Research Institute of the “Germans Trias i Pujol” Foundation, “Germans Trias i Pujol” Hospital, Autonoma University of Barcelona, Badalona, Spain
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  • Verónica Saludes,

    1. Microbiology Service, Health Sciences Research Institute of the “Germans Trias i Pujol” Foundation, “Germans Trias i Pujol” Hospital, Autonoma University of Barcelona, Badalona, Spain
    2. Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Barcelona, Spain
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  • Ramón Planas,

    1. Liver Unit, “Germans Trias i Pujol”, University Hospital, Badalona, Spain
    2. CIBER Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
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  • Fernando González-Candelas,

    1. Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Barcelona, Spain
    2. Joint Unit of Research in Genomics and Health CSISP-UVEG/Institut Cavanilles, Valencia, Spain
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  • Vicente Ausina,

    1. Microbiology Service, Health Sciences Research Institute of the “Germans Trias i Pujol” Foundation, “Germans Trias i Pujol” Hospital, Autonoma University of Barcelona, Badalona, Spain
    2. Biomedical Research Centre Network on Respiratory Diseases (CIBERES), Bunyola, Spain
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  • Maria Alma Bracho

    1. Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Barcelona, Spain
    2. Joint Unit of Research in Genomics and Health CSISP-UVEG/Institut Cavanilles, Valencia, Spain
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Abstract

The hepatitis C virus (HCV) has been classified into six genotypes and more than 70 subtypes with distinct geographical and epidemiological distributions. While 18 genotype 2 subtypes have been proposed, only 5 have had their complete sequence determined. The aim of this study was to characterize HCV isolates from three patients from the Barcelona metropolitan area of Spain for whom commercial genotyping methods provided discordant results. Full-length genome sequencing was carried out for 2 of the 3 patients; for the third patient only partial NS5B sequences could be obtained. The generated sequences were subjected to phylogenetic, recombination, and identity analyses. Sequences covering most of the HCV genome (9398 and 9566 nt in length) were obtained and showed a 90.3% identity to each other at the nucleotide level, while both sequences differed by 17.5–22.6% from the other fully sequenced genotype 2 subtypes. No evidence of recombination was found. The NS5B phylogenetic tree showed that sequences from the three patients cluster together with the only representative sequence of the provisionally designed 2q subtype, which also corresponds to a patient from Barcelona. Phylogenetic analysis of the full coding sequence showed that subtype 2q was more closely related to subtype 2k. The results obtained in this study suggest that subtype 2q now meets the requirements for confirmed designation status according to consensus criteria for HCV classification and nomenclature, and its epidemiological value is ensured as it has spread among several patients in the Barcelona metropolitan area. J. Med. Virol. 83:820–826, 2011. © 2011 Wiley-Liss, Inc.

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