About: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery 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	Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery
Creator	Wang, Jing Hall, Richard Peacey, Matthew Ren, Xiaoyun Strydom, Hugo Yen, Seiha Bissielo, Ange Carter, Philip Huang, Q Moore, Nicole Todd, Angela
Source	Elsevier; Medline; PMC
abstract	Abstract The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.
has issue date	2014-01-31(xsd:dateTime)
bibo:doi	10.1016/j.jviromet.2013.08.035
bibo:pmid	24036074
has license	els-covid
sha1sum (hex)	bcb3d555b716591ca4b1659781b5bce0d58af482
schema:url	https://doi.org/10.1016/j.jviromet.2013.08.035
resource representing a document's title	Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery
has PubMed Central identifier	PMC7113663
has PubMed identifier	24036074
schema:publication	Journal of Virological Methods
resource representing a document's body	covid:bcb3d555b716591ca4b1659781b5bce0d58af482#body_text
is schema:about of	named entity 'RAPID' named entity 'REVIEW OF' named entity 'NEW' named entity 'SAMPLE PREPARATION' named entity 'BUT' named entity 'TYPES' named entity 'ANALYSIS' named entity 'VIRAL' named entity 'QUICK' named entity 'INVESTIGATED' named entity 'STUDIES' named entity 'PROVIDES' named entity 'ABSOLUTE' named entity 'CONSIDERATION' named entity 'DIFFERENT' named entity 'REVEALED' named entity 'PROBABILITY OF' named entity 'BACTERIAL' named entity 'BEING' named entity 'POTENTIAL' named entity 'FUTURE' named entity 'STEP' named entity 'PHYSICAL' named entity 'ANIMAL' named entity 'EITHER' named entity 'SEQUENCES' named entity 'METHOD' named entity 'COMPOSED OF' named entity 'HAVE' covid:arg/bcb3d555b716591ca4b1659781b5bce0d58af482 named entity 'DISCOVERY' named entity 'GIVEN' named entity 'VIRUS' named entity 'NEED FOR' named entity 'ATTENTION' named entity 'PREPARATION' named entity 'ENRICHMENT' named entity 'VIRUSES' named entity 'SIMPLE' named entity 'TECHNIQUES' named entity 'EVALUATION' named entity 'PRIOR TO' named entity 'NUCLEASE' named entity 'USING' named entity 'DETERMINED BY' named entity 'QUANTITIES' named entity 'UNCHANGED' named entity 'DISCOVERY' named entity 'LITTLE' named entity 'ENRICHMENT' named entity 'LOW-SPEED CENTRIFUGATION' named entity 'USUALLY' named entity 'CAPSID' named entity 'SAMPLE' named entity 'TO INCREASE' named entity 'DIAGNOSTIC' named entity 'LARGELY' named entity 'RNA VIRUSES' named entity 'ARTIFICIAL' named entity 'AVAILABLE' named entity 'DATA' named entity 'PUBLISHED' named entity 'USED' named entity 'COMBINATIONS' named entity 'RESEARCHERS' named entity 'APPLIED' named entity 'ENHANCE' named entity 'BACTERIA ' named entity 'TECHNIQUES' named entity 'TYPE OF SAMPLE' named entity 'TREATMENT'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software