title: Molecular characterization of a full genome Turkish hepatitis C virus 1b isolate (HCV-TR1): a predominant viral form in Turkey.
abstract: Based on direct sequencing information from 5'UTR and NS5B regions, we identified subtype lb as a predominant hepatitis C virus genome in Turkey, which affected more than 91% of 79 patients studied. Next, the full genome sequence of a Turkish lb isolate was obtained by the cloning of polypeptide-encoding region into 7 overlapping fragments. Turkish 1b isolate, which was named HCV-TR1, comprises 9361 nucleotides, including 306 nucleotides of 5'UTR, a single long open reading frame of 9033 nucleotides, and 22 nucleotides of 3'UTR. When compared to HCV lb polypeptide sequences available at GenBank, the predicted polypeptide displayed a total of 36 amino acid substitutions, of which 16 was specific for HCV-TR1 isolate. Despite these changes, major structural and functional motifs of HCV proteins were maintained in HCV-TR1. In contrast, HCV-TR1 displayed amino acid substitutions in 6 out of 9 major cytotoxic T-cell epitopes. These data suggest that HCV-TR1 encodes functionally intact viral proteins, but it also encodes altered viral epitopes, which may affect host immune-response.
authors.affiliation: Department of Molecular Biology and Genetics and BilGen Genetics and Biotechnology, Research and Development Center, Bilkent University, Ankara, Turkey,
authors.forename: Esra
authors.initials: E
authors.lastname: Yildiz
authors.forename: Asli
authors.initials: A
authors.lastname: Oztan
authors.forename: Funda
authors.initials: F
authors.lastname: Sar
authors.forename: Ergun
authors.initials: E
authors.lastname: Pinarbasi
authors.forename: Rengul
authors.initials: R
authors.lastname: Cetin-Atalay
authors.forename: Hikmet
authors.initials: H
authors.lastname: Akkiz
authors.forename: Mehmet
authors.initials: M
authors.lastname: Ozturk
mesh_terms: D000595:Amino Acid Sequence; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry; D005260:Female; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D016056:Immunodominant Epitopes / Q000737:chemistry; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014421:Turkey; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D016056:Immunodominant Epitopes; D014764:Viral Proteins