Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

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 depen...

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Bibliographic Details
Published in:Nucleic Acids Research 2015-07, Vol.43 (13), p.6191-6206
Main Authors: Aguiar, Eric Roberto Guimarães Rocha, Olmo, Roenick Proveti, Paro, Simona, Ferreira, Flavia Viana, de Faria, Isaque João da Silva, Todjro, Yaovi Mathias Honore, Lobo, Francisco Pereira, Kroon, Erna Geessien, Meignin, Carine, Gatherer, Derek, Imler, Jean-Luc, Marques, João Trindade
Format: Article
Language:English
Subjects:
Animals
Computational Biology
Contig Mapping
Female
Immunology
Insecta - genetics
Life Sciences
Ovary - virology
Plants - virology
RNA, Small Untranslated - chemistry
RNA, Viral - chemistry
Sequence Analysis, RNA
Vertebrates - virology
Viral Tropism
Viruses - genetics
Viruses - isolation & purification
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkv587