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ABSTRACT

Hepatitis C is an infectious disease affecting primarily the liver, caused by the hepatitis C virus (HCV) it is a blood borne virus and the most common modes of infection are through unsafe injection practices, inadequate sterilization of medical equipment. The phylogenetic analysis of HCV is determined by analyzing sequences of conserved genes based on the randomly selected sequences from database. Mutations in conserved genes bring considerable variation among HCV subtypes. An online available tool Drawgram was used for multiple sequence alignment (MSA) while the alignment was rechecked by using CLUSTAL W and further was analyzed for conserved region. This research will provide complete structural and some of the functional properties of mutated subtypes of HCV and can be helpful for designing vaccine the analyzed data also provide useful information of evolutionary pattern of HCV.

INTRODUCTION

Hepatitis C is an infectious liver disease of humans and chimpanzees and is caused by the HCV (Chen and Morgan, 2006). The infection is often asymptomatic especially in its early stages but once established, it can progress to advanced liver diseases such as liver fibrosis and ultimately cirrhosis. These liver diseases can further lead to other complications such as liver failure and liver cancer (Villano et al., 1999). The discovery of HCV in the late 1980s occurred without the aid of conventional tissue culture or classical virological methods other than the essential reliance of the chimpanzee model for propagation and initial definition of the infectious agent as an enveloped RNA virus. Reverse transcription and PCR amplification of a sub genomic fraction of the HCV genome lead to the initial genetic characterization of HCV as a putative member of the Flaviviridae family.

In Pakistan an alarming rate of HCV outbreaks have been reported. The previous estimates indicate that around 10 million people are infected with HCV in Pakistan (Raja and Janjua, 2008;...