Computational prediction of hybridization patterns between hepatitis C viral genome and human microRNAs

Hepatitis C virus (HCV) infection causes acute and chronic hepatitis leading to cirrhosis and hepatocellular carcinoma which are the major health problems around the world including Thai population. Many recent studies were shown an important role of microRNA (miRNA) to inhibit or promote viral replication. This study aimed to investigate human miRNAs and analyze hybridization patterns between cellular microRNA (miRNA) and whole genome of hepatitis C virus (HCV) especially genotypes 1a, 3a and 6. Computational prediction was performed by using miRBase and RNAhybrid. Candidate human miRNAs were analyzed based on minimum free energy (MFE) and hybridization patterns between HCV viral target genes and the miRNAs. An individual genotype of HCV was targeted by different miRNAs due to highly genetic variation among different genotypes of HCV. The genome of HCV genotypes 1a, 3a and 6 was served as a target for hybridization with 26, 34 and 32 human miRNAs, respectively. There were only 3 miRNAs including hsa-miR-24-3p (for genotypes 3a & 6), hsa-miR-624 (for genotypes 1a & 3a) and hsa-miR-1915-5p (genotypes 1a & 3a) target with multiple genotypes of HCV. The results revealed several candidate miRNAs that should be further confirmed by experimental analysis to ensure the effect of each candidate miRNAs. Nevertheless, the predicted miRNAs targeting HCV might be useful and have a potential role for inhibition of hepatitis C viral replication in the future.