About: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

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About: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels Goto Sponge NotDistinct Permalink

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
has title	The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels
Creator	Shipulin, German Khafizov, Kamil Artyushin, Ilya Ayginin, Andrey Blinova, Ekaterina Dedkov, Vladimir Matsvay, Alina Pimkina, Ekaterina Safonova, Marina Speranskaya, Anna
Source	Medline; PMC
abstract	Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.
has issue date	2018-08-12(xsd:dateTime)
bibo:doi	10.1155/2018/3248285
bibo:pmid	30158979
has license	cc-by
sha1sum (hex)	ddddc52ff6183d8092a992286fd64acb18cdf2bd
schema:url	https://doi.org/10.1155/2018/3248285
resource representing a document's title	The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels
has PubMed Central identifier	PMC6109506
has PubMed identifier	30158979
schema:publication	Adv Virol
resource representing a document's body	covid:ddddc52ff6183d8092a992286fd64acb18cdf2bd#body_text
is schema:about of	named entity 'STUDY' named entity 'reliable' named entity 'bacteria' named entity 'spectrum' named entity 'families' named entity 'sequencing' named entity 'bird' named entity 'Viral' named entity 'DE NOVO' named entity 'OLIGONUCLEOTIDE' named entity 'PANELS' named entity 'GENOME' named entity 'NEXT GENERATION SEQUENCING' named entity 'BIRD' named entity 'VARIANTS' named entity 'INVOLVED' named entity 'HAVE' named entity 'IMPOSSIBLE' named entity 'EFFICIENCY' named entity 'VARIABILITY' named entity 'NUCLEIC ACIDS' named entity 'ADDITION' named entity 'BIOINFORMATICS' named entity 'DEMONSTRATED' named entity 'DEVELOPMENT' named entity 'TO DETECT' named entity 'ENTIRE' named entity 'VARIOUS' named entity 'MODULE' named entity 'SPECTRUM' named entity 'SAMPLES' named entity 'PRIMER' named entity 'PANEL' named entity 'USING' named entity 'NGS' named entity 'COVERING' named entity 'PARTICULAR' named entity 'SEQUENCES' named entity 'SAMPLES' named entity 'DISEASES' named entity 'BUT' named entity 'VIRAL RNA' named entity 'MULTIPLEX' named entity 'SPECIFIC' named entity 'SPECIES' named entity 'APPLICATION' named entity 'TARGET' named entity 'FUNCTIONALITY' named entity 'PREVALENT' named entity 'STUDY' named entity 'DETECTION' named entity 'ORDERS' named entity 'DETECTION OF BACTERIA' named entity 'TECHNOLOGIES' named entity 'COMPUTATIONAL' named entity 'IDENTIFICATION' named entity 'VIRUS DETECTION' named entity 'VIRAL PATHOGENS' named entity 'DATA ANALYSIS' named entity 'BIOLOGICAL MATERIAL' named entity 'SUPERIOR' named entity 'LOW' named entity 'CREATE' named entity 'DIVERSITY' named entity 'OLIGONUCLEOTIDES' named entity 'FAMILIES' named entity 'ITS' named entity 'GENOMIC' named entity 'PCR' named entity 'GENUS' named entity 'PIPELINE' named entity 'THEIR'

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