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

Content Provider	Springer Nature Link
Author	Rajhi, Mouna Mejri, Selma Djebbi, Ahlem Chouaieb, Soufiene Cheikh, Imed Ben Yahia, Ahlem Sadraoui, Amel Hammami, Walid Azouz, Msaddak Ben Mami, Nabil Triki, Henda
Copyright Year	2013
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.
Starting Page	209
Ending Page	217
Page Count	9
File Format	PDF
ISSN	09208569
Journal	Virus Genes
Volume Number	48
Issue Number	2
e-ISSN	1572994X
Language	English
Publisher	Springer US
Publisher Date	2013-11-23
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	HCV Genotype 2 Subtypes Molecular epidemiology Tunisia North Africa Medical Microbiology Virology Plant Sciences
Content Type	Text
Resource Type	Article
Subject	Virology Genetics Medicine Molecular Biology

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