Nucleotide identity and variability among different Pakistani hepatitis C virus isolates

The variability within the hepatitis C virus (HCV) genome has formed the basis for several genotyping methods and used widely for HCV genotyping worldwide.

The aim of the present study was to determine percent nucleotide identity and variability in HCV isolates prevalent in different geographical regions of Pakistan.

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.

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.

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.