Molecular characterization of a full genome Turkish hepatitis C virus 1b isolate (HCV-TR1): a predominant viral form in Turkey.
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.
Yildiz
Esra
E
Department of Molecular Biology and Genetics and BilGen Genetics and Biotechnology, Research and Development Center, Bilkent University, Ankara, Turkey,
Oztan
Asli
A
Sar
Funda
F
Pinarbasi
Ergun
E
Cetin-Atalay
Rengul
R
Akkiz
Hikmet
H
Ozturk
Mehmet
M
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
D018984:Epitopes, T-Lymphocyte; D016056:Immunodominant Epitopes; D014764:Viral Proteins