title: Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host.
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.
authors.affiliation: Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France.
authors.forename: Eric Roberto Guimarães Rocha
authors.initials: ER
authors.lastname: Aguiar
authors.affiliation: Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France.
authors.forename: Roenick Proveti
authors.initials: RP
authors.lastname: Olmo
authors.affiliation: CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France.
authors.forename: Simona
authors.initials: S
authors.lastname: Paro
authors.affiliation: Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil.
authors.forename: Flavia Viana
authors.initials: FV
authors.lastname: Ferreira
authors.affiliation: Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil.
authors.forename: Isaque João da Silva
authors.initials: IJ
authors.lastname: de Faria
authors.affiliation: Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil.
authors.forename: Yaovi Mathias Honore
authors.initials: YM
authors.lastname: Todjro
authors.affiliation: Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Campinas, São Paulo, CEP 13083-886, Brazil.
authors.forename: Francisco Pereira
authors.initials: FP
authors.lastname: Lobo
authors.affiliation: Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil.
authors.forename: Erna Geessien
authors.initials: EG
authors.lastname: Kroon
authors.affiliation: CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Meignin
authors.affiliation: Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, Lancashire, LA1 4YQ, UK.
authors.forename: Derek
authors.initials: D
authors.lastname: Gatherer
authors.affiliation: CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France Institut d'Etudes Avancées de l'Université de Strasbourg (USIAS), 67084 Strasbourg Cedex, France.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Imler
authors.affiliation: Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil jtm@ufmg.br.
authors.forename: João Trindade
authors.identifier: http://orcid.org/0000-0002-3457-3320
authors.initials: JT
authors.lastname: Marques
mesh_terms: D000818:Animals; D020451:Contig Mapping; D005260:Female; D007313:Insecta / Q000235:genetics; D010053:Ovary / Q000821:virology; D010944:Plants / Q000821:virology; D058727:RNA, Small Untranslated / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D014714:Vertebrates / Q000821:virology; D056189:Viral Tropism; D014780:Viruses / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D058727:RNA, Small Untranslated; D012367:RNA, Viral