HCV is a small enveloped single-stranded RNA virus belonging to the Flaviviridae family and Hepacivirus genus . Other Flaviviridae members include the flaviviruses such as yellow fever virus, and pestiviruses, which are responsible, for example, for bovine viral diarrhea . The most closely related virus identified to date is GBV-B, which infects the tamarind, a new world monkey. GBV-B has also been tentatively classified as a Hepacivirus
. The HCV genome consists of approximately 9,600 bases, encoding a single polyprotein of approximately 3,000 amino acids, flanked by conserved 5'- and 3'-untranslated regions essential for replication and translation (Figure 2.1A). The genome is replicated in the cytoplasm by a virally encoded polymerase and translated by cellular machinery directed to the viral RNA by a highly structured internal ribosomal entry sequence (IRES)
The viral polyprotein comprises four structural proteins followed by six non-structural proteins. The structural proteins are: envelope glycoproteins E1 and E2, Core, and the small P7 ion channel [14, 15]. Another putative protein, F, is also encoded by an alternate reading frame in the structural protein region, but no function for the protein has been identified . The non-structural proteins are designated NS2-N5B. NS2/3 possesses an essential autoprotease activity, but it is still not clear whether NS2 itself has an independent function. The bifunctional NS3 protein consists of an N-terminal
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