Hepatitis C virus genotyping using 5' nuclease real-time PCR and probes with oligodeoxyinosine linkers

Hepatitis C virus (HCV) is the main reason for acute hepatic lesions, including cirrhosis and hepatocellular carcinoma. The selection of antiviral treatment schemes depends on the genotype of the virus. Therefore, the HCV genotyping method is included in routine laboratory examinations. We developed a technique of RT-PCR HCV genotyping with increased specificity to genotype due to the use of originally designed fluorescent probes with oligodeoxyinosine linkers. The application of this technique allows one to detect genotypes 1, 2, and 3 and groups of genotypes 4-6 with high accuracy and analytical sensitivity (100 IU/ml). Using our technique, we defined HCV genotypes in 285 clinical samples obtained from medical institutions of the Siberian region. Strains with genotypes 1 (45% of samples), 2 (6%), and 3 (49%) were detected. Our results were in accordance with the data obtained by sequencing and genotyping using commercial kits.