Virus Genes

, Volume 48, Issue 2, pp 209–217

Subtyping genotype 2 hepatitis C viruses from Tunisia: identification of two putative new subtypes

Authors

  • Mouna Rajhi
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Selma Mejri
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Ahlem Djebbi
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Soufiene Chouaieb
    • Departement of GastroenterologyHôpital La Rabta
  • Imed Cheikh
    • Departement of GastroenterologyHôpital Bizerte
  • Ahlem Ben Yahia
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Amel Sadraoui
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Walid Hammami
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
  • Msaddak Azouz
    • Departement of GastroenterologyHôpital Nabeul
  • Nabil Ben Mami
    • Departement of GastroenterologyHôpital La Rabta
    • Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and MeaslesInstitute Pasteur de Tunis
Article

DOI: 10.1007/s11262-013-1010-3

Cite this article as:
Rajhi, M., Mejri, S., Djebbi, A. et al. Virus Genes (2014) 48: 209. doi:10.1007/s11262-013-1010-3
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Abstract

HCV variants were classified into six genotypes (1–6) subdivided into several subtypes with different geographic distribution worldwide. Previous studies conducted in Tunisia showed that genotype 1 counts for more than 80 % of circulating HCV genotypes and most of the isolates belong to subtype 1b. Genotype 2 comes in the second position, however, few sequences have been analyzed and published. In the present study, 89 isolates from Tunisian patients, typed as genotype 2 by the InnoLIPA commercial probe hybridization test, were sequenced in the NS5B and Core/E1 regions. All the isolates, clustered with the genotype 2 reference sequences, in the NS5B and in the Core/E1 region and the phylogenetic analyses in the two genomic regions were perfectly concordant: subtype 2c was the most frequent (58 out of 89, 65.1 %) and few isolates belonged to subtypes 2k(n = 10), 2i(n = 5), and 2b(n = 1). Fifteen isolates did not match with any of the reference sequences representing the genotype 2 subtypes, identified up-to-date. They divided into 2 separate clusters with high bootstrap values in both genomic regions. This study shows perfect concordance between the NS5B and the Core/E1 region suggesting that any of the two regions can be used for genotyping and that intergenotypic and intragenotypic recombinants are not very frequent, at least for HCV isolates from genotype 2. The present study also shows a predominance of subtype 2c among genotype 2 HCV isolates circulating in Tunisia, the co-circulation of minor subtypes (2k, 2i, and 2b) and proposes the possible existence of two other new subtypes.

Keywords

HCVGenotype 2SubtypesMolecular epidemiologyTunisiaNorth Africa

Copyright information

© Springer Science+Business Media New York 2013