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  • Aguiar et al final version

    Rights statement: 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

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

Research output: Contribution to journalJournal articlepeer-review

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  • Eric Roberto Guimarães Rocha Aguiar
  • Roenick Proveti Olmo
  • Simona Paro
  • Flavia Viana Ferreira
  • Isaque João da Silva de Faria
  • Yaovi Mathias Honore Todjro
  • Francisco Pereira Lobo
  • Erna Geessien Kroon
  • Carine Meignin
  • Derek Gatherer
  • Jean-Luc Imler
  • João Trindade Marques
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<mark>Journal publication date</mark>3/06/2015
<mark>Journal</mark>Nucleic Acids Research
Issue number13
Volume43
Number of pages16
Pages (from-to)6191–6206
Publication StatusPublished
Early online date3/06/15
<mark>Original language</mark>English

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.

Bibliographic note

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