title: Hepatitis C virus genotype distribution in Turkey remains unchanged after a decade: performance of phylogenetic analysis of the NS5B, E1, and 5'UTR regions in genotyping efficiency.
abstract: OBJECTIVE
  Hepatitis C virus (HCV) genotyping has a considerable effect on therapy. The aim was to determine the change in prevalence of HCV genotypes in Turkey during the last decade and to compare the performance of DNA sequencing of different targets in the HCV genome (NS5B, E1, and 5'UTR).
  
  
  METHODS
  Five hundred HCV RNA-positive patients (226 males, 274 females) were included in the study. The NS5B, E1, and 5'UTR regions of the HCV genome were amplified by polymerase chain reaction (PCR) in patients where possible. Amplified PCR products were sequenced directly, and phylogenetic analysis was performed. A commonly used database, namely www.hcv.lanl.gov, was also used to determine the genotypes.
  
  
  RESULTS
  Phylogenetic analysis of the NS5B, E1, and 5'UTR regions showed that 1b was the most frequent genotype, with percentages of 92.5%, 93.5%, and 87.7%, respectively. Genotype 1a was the second most prevalent genotype, with ratios of 6.7%, 5.6%, and 6.6%, whereas genotype 2a was detected in proportions of 0.4%, 0.2%, and 0.8%, respectively. Genotype 5 or 6 was not detected among patients. The phylogenetic analysis showed discordant results with 18 patients' genotypes for different targets. The phylogenetic analysis showed similar results with the hcv.lanl.gov database for the E1 and NS5B sequences.
  
  
  CONCLUSIONS
  There has been no change in genotyping profiles of Turkey during the last decade, representing 1b as the most prevalent subtype, followed by 1a. Phylogenetic analysis of HCV indicated high performance compared with the hcv.lanl.gov database when sequences of E1 and NS5B regions were analyzed.
authors.affiliation: Institute of Hepatology, Ankara University Faculty of Medicine, Ankara, Turkey. mithat.bozdayi@medicine.ankara.edu.tr.
authors.forename: Gökçe
authors.initials: G
authors.lastname: Kabakçı Alagöz
authors.forename: Senem Ceren
authors.initials: SC
authors.lastname: Karataylı
authors.forename: Ersin
authors.initials: E
authors.lastname: Karataylı
authors.forename: Esra
authors.initials: E
authors.lastname: Celik
authors.forename: Onur
authors.initials: O
authors.lastname: Keskin
authors.forename: Bedia
authors.initials: B
authors.lastname: Dinç
authors.forename: Kubilay
authors.initials: K
authors.lastname: Cınar
authors.forename: Ramazan
authors.initials: R
authors.lastname: Idilman
authors.forename: Cihan
authors.initials: C
authors.lastname: Yurdaydın
authors.forename: A Mithat
authors.initials: AM
authors.lastname: Bozdayı
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D000368:Aged; D005260:Female; D005838:Genotype; D060005:Genotyping Techniques; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D058974:Phylogeography; D017422:Sequence Analysis, DNA / Q000379:methods; D013997:Time Factors; D014421:Turkey; D014759:Viral Envelope Proteins / Q000235:genetics*; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D014759:Viral Envelope Proteins; D017361:Viral Nonstructural Proteins; C087035:E1 protein, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase