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

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host
Creator	Gatherer, Derek Marques, João Imler, Jean-Luc Meignin, Carine Paro, Simona Ferreira, Flavia João Da Silva De Faria, Isaque Kroon, Erna Mathias, Yaovi Olmo, Roenick Pereira Lobo, Francisco Roberto, Eric Rocha Aguiar, Guimarães Todjro, Honore
source	Medline; PMC
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.
has issue date	2015-07-27(xsd:dateTime)
bibo:doi	10.1093/nar/gkv587
bibo:pmid	26040701
has license	cc-by
sha1sum (hex)	52879771bf3fb8b982308b90d70bebd2485ceaf1
schema:url	https://doi.org/10.1093/nar/gkv587
resource representing a document's title	Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host
has PubMed Central identifier	PMC4513865
has PubMed identifier	26040701
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:52879771bf3fb8b982308b90d70bebd2485ceaf1#body_text
is schema:about of	named entity 'SEQUENCE' named entity 'wild' named entity 'detection' named entity 'viral' named entity 'based' named entity 'sequences' named entity 'vertebrates' named entity 'great' named entity 'virus' named entity 'strategy' named entity 'sequences' named entity 'RNAs' named entity 'HOST RESPONSE' named entity 'COMPARISON' named entity 'RNA PROFILE' named entity 'GREAT' named entity 'HERE' named entity 'LONG' named entity 'BASED' named entity 'VERTEBRATES' named entity 'SIZE' named entity 'POPULATIONS' named entity 'IDENTIFICATION' named entity 'WILD' named entity 'PREVIOUSLY' named entity 'PUBLIC HEALTH' named entity 'STRATEGY' named entity 'CHARACTERIZED' named entity 'OUR' named entity 'COULD BE' named entity 'BENEFIT' named entity 'MOSQUITOES' named entity 'INDEPENDENT' named entity 'SMALL' named entity 'USED' named entity 'VIRUS' named entity 'INDEPENDENT' named entity 'RELATIVES' named entity 'VECTOR' named entity 'NOVEL' named entity 'VIRAL' named entity 'HOST' named entity 'VIRUSES' named entity 'INSECT VECTORS' named entity 'FRUIT FLIES' named entity 'LARGELY' named entity 'RNA INTERFERENCE PATHWAY' named entity 'RESULTS' named entity 'SMALL RNA' named entity 'BIOLOGY' named entity 'SANDFLIES' named entity 'KNOWN' named entity 'USING' named entity 'SEQUENCE' named entity 'FORMAL' named entity 'ENRICHED' named entity 'PLANTS' named entity 'SUGGEST' named entity 'TO IDENTIFY' named entity 'REFERENCE' named entity 'NOTED' named entity 'VIRUSES' named entity 'VIRAL' named entity 'LARGE-SCALE SEQUENCING' named entity 'VIRUS DETECTION' named entity 'DATABASES' named entity 'STRATEGIES' named entity 'BUT'

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