HCV-Core Region: Its Significance in HCV-Genotyping and Type Dependent Genomic Expression

Present study reports the standardization and use of polymerase chain reaction (PCR) followed by RFLP (PCR-RFLP) implicating HCV-core as a target region and its comparison with PCR-RFLP based on the use of 5'NCR for HCV genotyping / sub-typing. The new assay produced 399bp PCR product from core region and used a different set of restriction enzymes (MboI, AccI and BstNI) to digest these products for HCV sub-typing. This assay allows a quick determination of HCV types / sub-types. HCV was typed / sub-typed using these two assays in patients with liver and renal diseases. Analysis of results demonstrated the two assay system to be comparable with some difference in few cases. Whereas genotype-3 was a common finding in liver disease groups, genotype-1 was more frequent in chronic renal failure cases. The PCR product from core based assays was also subjected to sequence analysis for genotypes/sub-types and the findings were slightly different. This was further analysed by phylogenetic analysis which supported our findings.