Human picobirnaviruses identified by molecular screening of diarrhea samples.

The global threat of (re)emerging infectious viruses requires a more effective approach regarding virus surveillance and diagnostic assays, as current diagnostics are often virus species specific and not able to detect highly divergent or unknown viruses. A systematic exploration of viruses that infect humans is the key to effectively counter the potential public health threat caused by new and emerging infectious diseases. The human gut is a known reservoir of a wide variety of microorganisms, including viruses. In this study, Dutch clinical diarrhea samples for which no etiological agent could be identified by available cell culture, serological, or nucleic acid-based tests were gathered. Large-scale molecular RNA virus screening based on host nucleic acid depletion, sequence-independent amplification, and sequencing of partially purified viral RNA from a limited number of clinical diarrhea samples revealed four eukaryotic virus species. Among the detected viruses were a rhinovirus and a new picobirnavirus variant. In total, approximately 20% of clinical diarrhea samples contained human picobirnavirus sequences. The Dutch picobirnaviruses belonged to different phylogenetic clades and did not group with other picobirnaviruses according to year of isolation or host species. Interestingly, the average age of patients infected with picobirnavirus was significantly higher than that of uninfected patients. Our data show that sequence-independent amplification of partially purified viral RNA is an efficient procedure for identification of known and highly divergent new RNA viruses in clinical diarrhea samples.

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.