Real time pcr for genotyping of hepatitis c virus: evaluation and application

Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. It is associated with the development of end-stage liver disease and hepatocellular carcinoma. Studies have shown that patients infected with different genotypes of HCV may respond to different antiviral therapy differently and thus HCV genotype information is very important in helping physicians to better managing their patients. The aim of the study was to evaluate a real time PCR HCV genotyping assay against a nested RT PCR. The results indicated that real time PCR is feasible, easier and more sensitive than the nested RT PCR. A total of 96 samples were genotyped by both methods. Both methods detected HCV genotype 1 in 32 samples, genotype 4 in 39 samples, HCV enotype 3 in 19 samples, HCV genotype 2 were detected by nested RT PCR in 2 samples and 6 samples by real time PCR. The results showed that 100% sensitivity of HCV genotypes was observed with real time PCR technique and only 95.8% sensitivity of HCV genotypes was observed with nested PCR technique. The most commonly detected genotypes in 96 positive HCV plasma samples was genotype G4 (40.6 %), followed by genotype G1 (33.3%) with the predominant subtype 1a (21.8%) and subtype 1b (11.5%). The genotype 2 was detected in 6% of patients, HCV genotype 3 was detected in 19.8% of the tested plasma samples. Real time PCR seems to be reliable diagnostic method for genotyping of HCV isolates.