Determination of HCV quasispecies by cloning and sequencing

Most RNA viruses exists as a heterogeneous mixture of closely related viral genome in the host, which is the result of high error rates in RNA replication and selected by various viral and host factors. The spectrum of this spectrum of related genomes within a host is referred as quasispecies (1). This important biological characteristics of RNA virus is believed to contribute to viral persistence in the presence of host immune system and during treatment with antiviral agents. Hepatitis C virus (HCV), being a single-strand RNA virus, is no exception. In HCV genome, the most heterogeneous regions he within the envelope 2 region, which are referred to as hypervariable regions (HVRs). The HVRs in HCV are believed to be the result of high nucleotide variation and immune selection pressure (2). Because of its heterogeneity, this is a good region for the study of HCV quasispecies.