ABSTRACT
Hepatitis C virus (HCV) is a positive sense virus with a genomic RNA molecule roughly
9,600 nucleotides in length. The single-stranded genomic RNA has a nontranslated region
(NTR) at each end and a long open reading frame (coding region) in between. The 5′NTR
and portions of the 3′NTR are the most conserved parts of HCV RNA. These conserved
regions contain signals for replication and translation. Much of the 5′NTR is folded
into a structure that binds ribosomes. This structure, an internal ribosome entry
site, promotes the initiation of protein synthesis and is critical for HCV gene expression.
The ribosome binding site may extend into the coding region; its exact boundaries
are not known. The open reading frame encodes the HCV polyprotein, which is slightly
more than 3,000 amino acids in length. The 3′NTR plays a key role in HCV replication
and may also influence the rate of HCV protein synthesis. During replication, the
genomic RNA is copied by virally encoded enzymes into a complementary antigenomic
RNA, which itself is a template for the synthesis of progeny RNAs. At steady state,
genomic strands outnumber antigenomic strands about 10 to 1. HCV RNA replication is
thought to take place in the cytoplasm and is an error-prone process. It generates
a mixed population of RNA sequences (quasispecies), including mutants that may be
more fit than the parental type, less fit, or equally fit (but distinct). Natural
selection acts upon the progeny RNAs, causing the population to change and drift.
Over time, mutation, selection, and population bottlenecks led to the evolution of
varied genotypes. The HCV replication complex is a potential source of double-stranded
RNA, a powerful inducer of interferon. Thus, HCV-specific double-stranded RNA may
trigger the first steps of innate immunity; however, for unknown reasons, the immune
system often fails to clear the infection. The plasticity of the HCV genome and the
low level of HCV gene expression may counterbalance any immunostimulatory effects
of HCV RNA and allow the virus to escape specific immune responses. Antisense drugs
and ribozymes directed against HCV RNA are under investigation. Future interventions
may include nucleic acid drugs (antisense and ribozymes) and smaller pharmaceuticals
that bind to intricate structures in HCV RNA and HCV-specific double-stranded RNA.
Infectious clones of HCV RNA are available. These clones and other systems for expressing
HCV proteins pave the way for vaccine development.
KEYWORD
internal ribosome entry site - double-stranded RNA - interferon - antisense
