In Vitro Stability of Hepatitis C Virus RNA

Hepatitis C virus (HCV) is an encapsidated RNA virus, known to cause devastating liver diseases among the majority of infected individuals (1 –3 ). Latest breakthrough in molecular technology has greatly assisted the advancement in diagnostics and monitoring of virological response to therapy (4 ). However, our understanding of the pathogenesis and replication of HCV has been impeded by the immense difficulty in cultunng the virus in vitro and the lack of a small animal model. One of the possible explanations for this observation is the instability of the HCV RNA genome in vivo and in vitro. In 1996, two independent research teams described an extended 3′ untranslated region (UTR) that is conserved among most HCV genotypes and had been missing in all published sequences prior to this discovery (5 ,6 ). There has been speculation concerning its role in stabilizing the HCV RNA genome and in the initiation of the synthesis of the nascent minus RNA strand. In this chapter, a simple in vitro assay is used to analyze the stabilization effect of the various forms of the HCV 3′ UTR that have been described in the literature.