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.
Aim: 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.
Conclusion: 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.