Hepatitis C Viral Heterogeneity Based on Core Gene and an Attempt to Design Small Interfering RNA Against Strains Resistant to Interferon in Rawalpindi, Pakistan

Abstract

Background Global prevalence of Hepatitis C Virus (HCV) infection corresponds to about 130 million HCV positive patients worldwide. The only drug that effectively reduces viral load is interferon-α (IFN-α) and currently combination of IFN and ribavirin is the choice for treatment. Objectives The present study is aimed to resolve the genotypes based on core gene that might affect the response to interferon therapy. Furthermore an attempt was made to propose a powerful therapeutic approach by designing the siRNA from sequences of the same patients who remain resistant to IFN in this study. Patients and Methods To achieve the objectives, a sequence analysis was performed in five HCV ELISA positive subjects who have completed IFN treatment. Neighbor Joining (NJ) method was used to study the evolutionary relationship. Atomic models were predicted using online software PROCHECK and i- TASSER. Results Two new genotypes were reported for the first time namely 4a from suburban region of Rawalpindi and 6e from all over the Pakistan. According to Ramachandran plot, satisfactory atomic model was considered useful for further studies, i.e. to calculate HCV genotypes conservation at structural level, to find out critical binding sites for drug designing, or to silence those binding sites by using appropriate siRNA. Single siRNA can be used to inhibit HCV RNA synthesis against genotype 3 and 4, as the predicted siRNA were originated from the same domain in studied HCV core region in both genotypes. Conclusions We can conclude that any change or mutation in core region might be the cause of HCV strains to resist against IFN therapy. Therefore, further understanding of the complex mechanism involved in disrupting viral response to therapy would facilitate the development of more effective therapeutic regimens. Additionally, a single designed siRNA can be used as an alternative for current therapy against more than one resistant HCV genotypes.

Molecular characterization of Hepatitis C virus 3a in Peshawar

“…A representative number of samples (58/192), which turned out positive for HCV 3a by the Type-specific assay described earlier, were used for a second round of RNA extraction, RT PCR and subsequent regular nested PCR for the amplification of Core gene using gene-specific primer [ 24 ].…”

Hepatitis C virus resistance to interferon therapy: an alarming situation

“…Hyper-variability of virus envelope protein fails the successful clearance of virus from patient's body and facilitates HCV to neutralize antibody. HCV core protein is reported to be involved in reducing the robustness of the host's immune response as it decreases the transcription of interferon induced antiviral genes [27]. Inhibition of amplifi cation loop of IFN might be harmed by HCV NS3/4A protease which otherwise can inhibit HCV replication.…”