title: Hepatitis C virus of subtype 2l in Marseille, southeastern France.
abstract: The rate of eradication of chronic hepatitis C considerably increases with direct-acting antiviral agents, particularly hepatitis C virus (HCV) polymerase inhibitors. While implementing full-length HCV NS5B polymerase sequencing in our clinical microbiology laboratory, we identified atypical HCV sequences, classified as subtype 2l, from 2 patients. HCV-2l NS5B polymerase sequences were detected from 5 and 14 additional patients by screening our laboratory hepatitis virus sequence database and the NCBI GenBank sequence database. Phylogenetic analyses show unambiguously that all HCV-2l sequences are clustered apart from HCV 2 non-l sequences, which compose a second cluster. Mean (±SD) nucleotide identity between near full-length NS5B fragments of subtype 2l was 93.4 ± 0.8% (range: 92.4-95.1). Of note, all HCV-2l sequences obtained in our laboratory and in other centers were from serum samples collected in France. Analysis of the HCV-2l NS5B polymerase amino acid sequences at 30 positions critical for interaction with or resistance to HCV polymerase inhibitors showed specific patterns.
authors.affiliation: URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille University, Marseille, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Aherfi
authors.forename: Olga
authors.initials: O
authors.lastname: Glazunova
authors.forename: Patrick
authors.initials: P
authors.lastname: Borentain
authors.forename: Daniele
authors.initials: D
authors.lastname: Botta-Fridlund
authors.forename: Laurent
authors.initials: L
authors.lastname: Chiche
authors.forename: Sylvie
authors.initials: S
authors.lastname: Bregigeon
authors.forename: Anne
authors.initials: A
authors.lastname: Motte
authors.forename: Catherine
authors.initials: C
authors.lastname: Tamalet
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
mesh_terms: D000328:Adult; D000369:Aged, 80 and over; D000595:Amino Acid Sequence; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D005260:Female; D005602:France; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D019698:Hepatitis C, Chronic / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000145:classification / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase