RNA secondary structures in the proximal 3′UTR of Indonesian Dengue 1 virus strains

The characteristics of DENV-1 viruses, isolated during the 2001–2002 outbreak in Indonesia were studied. The secondary structure of the 3′UTR of different DENV-1 strains derived from Indonesian patients was compared with the 3′UTR of previously described DENV-1 sequences. The complete 3′UTR of DENV-1 was sequenced from 13 patients suffering from the severe form of dengue virus infection (dengue hemorrhagic fever). Prediction of RNA secondary structure of the 3′UTR revealed some previously unidentified conserved structures in the proximal region of the 3′UTR, the role of which in viral replication is still unknown. In addition our data suggest that some structural elements previously described in the distal part of the 3′UTR are partly dependent on the proximal part of the UTR. Our data support the existence of previously unidentified conserved secondary structures in the proximal part of the 3′UTR and their roles need to be further investigated.