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In our country Pakistan, despite intensive awareness, treatment and prevention programs by public sector and NGO’s, rapidly increasing rate of HCV infection has evolved as an epidemic over last decade. Genotype 3a predominantly found in Pakistan. The objective of this study was to analyze structural changes in NS5A region of HCV 3a genome and the subsequent possible outcome. We included five hundred patients in our study. Results of 12 selected samples being presented here. The gender selection was random, ratio of male to female patients was nearly equal. The study was performed in Department of Biotechnology, University of Karachi where nested PCR of HCV seropositive isolates was performed. Other lab parameters were carried out in Rahila Diagnostic Research and Reference lab (pvt) Ltd; including qualitative & quantitative RT-PCR and genotyping. We analyzed NS5A region in the span of residues (2213-2352) including the ISDR, PKRBD & short sequence outside PKRBD (2281-2335). Multiple mutations have been found. The most notable substitutions found in this region was Proline to Leucine (P2274L). The peptide epitopes in NS5A have been studied abroad in the context of vaccine development against HCV. Effective vaccine development is the major demand in healthcare field for therapy & prevention of HCV. Our study on HCV genotype 3a along with other peer research work in our country and other parts of world would provide new parameters and better understanding of structural changes in NS5A region of HCV genome that would be helpful to modulate therapeutic approach and vaccine preparation against Hepatitis C virus. In addition, it demonstrates the importance of application of bioinformatics tools for the study of proteins that are difficult to be investigated by other experimental procedures.

Molecular Characterization of HCV NS5A in Patients Receiving Interferon Therapy