title: Nucleotide identity and variability among different Pakistani hepatitis C virus isolates.
abstract: BACKGROUND
  The variability within the hepatitis C virus (HCV) genome has formed the basis for several genotyping methods and used widely for HCV genotyping worldwide.
  
  
  OBJECTIVE
  The aim of the present study was to determine percent nucleotide identity and variability in HCV isolates prevalent in different geographical regions of Pakistan.
  
  
  METHODS
  Sequencing analysis of the 5'noncoding region (5'-NCR) of 100 HCV RNA-positive patients representing all the four provinces of Pakistan were carried out using ABI PRISM 3100 Genetic Analyzer.
  
  
  RESULTS
  The results showed that type 3 is the predominant genotypes circulating in Pakistan, with an overall prevalence of 50%. Types 1 and 4 viruses were 9% and 6% respectively. The overall nucleotide similarity among different Pakistani isolates was 92.50% +/- 0.50%. Pakistani isolates from different areas showed 7.5% +/- 0.50% nucleotide variability in 5'NCR region. The percent nucleotide identity (PNI) was 98.11% +/- 0.50% within Pakistani type 1 sequences, 98.10% +/- 0.60% for type 3 sequences, and 99.80% +/- 0.20% for type 4 sequences. The PNI between different genotypes was 93.90% +/- 0.20% for type 1 and type 3, 94.80% +/- 0.12% for type 1 and type 4, and 94.40% +/- 0.22% for type 3 and type 4.
  
  
  CONCLUSIONS
  Genotype 3 is the most prevalent HCV genotype in Pakistan. Minimum and maximum percent nucleotide divergences were noted between genotype 1 and 4 and 1 and 3 respectively.
authors.affiliation: National Centre of Excellence in Molecular Biology, 87-West Canal Bank Road Thokar Niaz Baig Lahore-53700, University of the Punjab Lahore, Pakistan. idreeskhan96@yahoo.com
authors.forename: Muhammad
authors.initials: M
authors.lastname: Idrees
authors.forename: Sadia
authors.initials: S
authors.lastname: Butt
authors.forename: Zunaira
authors.initials: Z
authors.lastname: Awan
authors.forename: Mahwish
authors.initials: M
authors.lastname: Aftab
authors.forename: Bushra
authors.initials: B
authors.lastname: Khubaib
authors.forename: Irshad-Ur
authors.initials: IU
authors.lastname: Rehman
authors.forename: Madiha
authors.initials: M
authors.lastname: Akram
authors.forename: Sobia
authors.initials: S
authors.lastname: Manzoor
authors.forename: Haji
authors.initials: H
authors.lastname: Akbar
authors.forename: Shazia
authors.initials: S
authors.lastname: Rafiqe
authors.forename: Sheikh
authors.initials: S
authors.lastname: Riazuddin
mesh_terms: D020121:5' Untranslated Regions; D000293:Adolescent; D000328:Adult; D000368:Aged; D001483:Base Sequence; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D055815:Young Adult
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral
references.citation: J Gastroenterol Hepatol. 1997 Nov;12(11):758-61
references.pmid: 9430043
references.citation: J Dig Dis. 2008 May;9(2):95-103
references.pmid: 18419643
references.citation: J Med Virol. 2004 Oct;74(2):246-52
references.pmid: 15332273
references.citation: Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11022-6
references.pmid: 7972001
references.citation: BMC Infect Dis. 2008 May 23;8:69
references.pmid: 18498666
references.citation: Bioinformatics. 2001 Dec;17(12):1244-5
references.pmid: 11751241
references.citation: J Gen Virol. 1995 Oct;76 ( Pt 10):2493-507
references.pmid: 7595353
references.citation: J Clin Microbiol. 1994 Dec;32(12):3049-51
references.pmid: 7883898
references.citation: J Gen Virol. 1997 Jun;78 ( Pt 6):1341-7
references.pmid: 9191927
references.citation: J Clin Microbiol. 2004 Jan;42(1):158-63
references.pmid: 14715747
references.citation: J Hepatol. 1996 Aug;25(2):212-7
references.pmid: 8878784
references.citation: Semin Liver Dis. 1995 Feb;15(1):41-63
references.pmid: 7597443
references.citation: J Gen Virol. 1993 Nov;74 ( Pt 11):2385-90
references.pmid: 7504073
references.citation: Hepatology. 2003 Apr;37(4):802-9
references.pmid: 12668973