Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host.
Fiche publication
Date publication
juillet 2015
Journal
Nucleic acids research
Auteurs
Membres identifiés du Cancéropôle Est :
Pr IMLER Jean-Luc, Dr MEIGNIN Carine
Tous les auteurs :
Aguiar ER, Olmo RP, Paro S, Ferreira FV, de Faria IJ, Todjro YM, Lobo FP, Kroon EG, Meignin C, Gatherer D, Imler JL, Marques JT
Lien Pubmed
Résumé
Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.
Mots clés
Animals, Contig Mapping, Female, Insecta, genetics, Ovary, virology, Plants, virology, RNA, Small Untranslated, chemistry, RNA, Viral, chemistry, Sequence Analysis, RNA, Vertebrates, virology, Viral Tropism, Viruses, genetics
Référence
Nucleic Acids Res.. 2015 Jul 27;43(13):6191-206