TY - JOUR

T1 - Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

AU - Aguiar, Eric Roberto Guimarães Rocha

AU - Olmo, Roenick Proveti

AU - Paro, Simona

AU - Ferreira, Flavia Viana

AU - de Faria, Isaque João da Silva

AU - Todjro, Yaovi Mathias Honore

AU - Lobo, Francisco Pereira

AU - Kroon, Erna Geessien

AU - Meignin, Carine

AU - Gatherer, Derek

AU - Imler, Jean-Luc

AU - Marques, João Trindade

N1 - 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

PY - 2015/6/3

Y1 - 2015/6/3

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkv587

DO - 10.1093/nar/gkv587

M3 - Journal article

C2 - 26040701

VL - 43

SP - 6191

EP - 6206

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 13

ER -