ral ssBioMed CentVirology Journal Open AcceResearch Nucleotide identity and variability among different Pakistani

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