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

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.

Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

“…The frequency of HCV-2c varies from one country to another. Although not very common in Brazil, Canada, Chile, Mexico, or the USA [ 37 , 38 ], HCV-2c is the second most frequently isolated after genotype 1 in Argentina [ 39 ], Italy [ 40 ] and in Tunisia [ 19 ]. In the present work, we analyzed the genetic diversity and the phylogenetic relatedness between the NS5B sequences within HCV-2c subtype.…”

“…The reliability of the phylogenetic constructions was estimated by bootstrap analysis with 1000 pseudo replicate data sets. Sixty-eight out of the 113 Tunisian sequences included in the present study were previously published in GenBank [ 19 ] whereas 45 sequences are new and reported for the first time in this study; they were submitted to GenBank under the accession numbers KJ206290 to KJ206333 and KJ206335. In addition, ninety-two HCV field sequences, published in GenBank and isolated from different countries in the world were included in these phylogenetic analyses: 53 isolates from Subtype 2c and 39 isolates from subtype 2k.…”

“…In Tunisia, Genotype 1 is the most prevalent, representing 70 to 80% and Genotype 2 comes in the second position with approximately 10% of circulating isolates [ 16 – 18 ]. In a recently published study, we showed that most of HCV-2 isolates belong to subtype 2c with few co-circulating isolates from other subtypes, especially 2k [ 19 ]. The aim of the present study was to analyse the genetic diversity and to reconstruct the genetic history of the most prevalent HCV-2 subtypes.…”