Flaviviruses are enveloped viruses with a single-stranded, 10.7kb positive-sense RNA genome. The genomic RNA, which has a 5' cap but no poly(A) tail, is translated as a single polyprotein that is then cleaved into three structural proteins and seven non-structural (NS) proteins by both viral and host proteases. The NS proteins include an RNA-dependent RNA polymerase (NS5), a helicase/protease (NS3), and other proteins that form part of the viral replication complex. Sequences and structures in the 5' and 3' untranslated regions (UTR) and capsid gene, including the cyclization sequences, the upstream AUG region, and the terminal 3' stem-loop, regulate translation, RNA synthesis and viral replication. We have also found that an RNA hairpin structure in the capsid coding region (cHP) influences start codon selection and viral replication of the flavivirus dengue virus (DENV). Peptide-conjugated phosphorodiamidate morpholino oligomers (P-PMOs) were used to further dissect the role of conserved regions of the 5' and 3' UTRs; several P-PMOs were shown to specifically inhibit DENV translation and/or RNA synthesis and, hence, are potentially useful as antiviral agents. Regarding the mechanism of DENV translation, we have shown that DENV undergoes canonical cap-dependent translation initiation as well as a non-canonical mechanism when cap-dependent translation is suppressed. Although much remains to be elucidated about the molecular biology of flavivirus infection, progress is being made towards defining the cis and trans factors that regulate flavivirus translation and replication.
Harris E, Holden KL, Edgil D, Polacek C, Clyde K. (2006). Molecular biology of flaviviruses. Novartis Foundation symposium, (277)