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

Aguiar, Eric Roberto Guimarães Rocha and Olmo, Roenick Proveti and Paro, Simona and Ferreira, Flavia Viana and de Faria, Isaque João da Silva and Todjro, Yaovi Mathias Honore and Lobo, Francisco Pereira and Kroon, Erna Geessien and Meignin, Carine and Gatherer, Derek and Imler, Jean-Luc and Marques, João Trindade (2015) Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Nucleic Acids Research. ISSN 0305-1048

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Abstract

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.

Item Type:
Journal Article
Journal or Publication Title:
Nucleic Acids Research
Additional Information:
This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Nucleic Acids Research following peer review. The definitive publisher-authenticated version Aguiar, et al., Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host, Nucleic Acids Research, 2015, is available online at: http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv587
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1300/1311
Subjects:
ID Code:
74124
Deposited By:
Deposited On:
22 Jun 2015 11:28
Refereed?:
Yes
Published?:
Published
Last Modified:
26 Sep 2020 03:21