About: Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

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About: Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing 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 Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
Creator	Lukjancenko, Oksana Girones, Rosina Bofill-Mas, Sílvia Elsässer, Dennis Fernandez-Cassi, Xavier Hellmér, Maria Seidel, Michael Timoneda, Natàlia Aarestrup, Frank Hjort, Mathis Schultz, Anna Abril, Josep Lö Fströ M 2¤, Charlotta
Source	PMC
abstract	Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS(®) miniMAG(®), or PowerViral(®) Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral(®) Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
has issue date	2017-01-18(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0170199
bibo:pmid	28099518
has license	cc-by
sha1sum (hex)	3b5ea760c63aaff964de32541643d92c69dfc05e
schema:url	https://doi.org/10.1371/journal.pone.0170199
resource representing a document's title	Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
has PubMed Central identifier	PMC5242460
has PubMed identifier	28099518
schema:publication	PLoS One
resource representing a document's body	covid:3b5ea760c63aaff964de32541643d92c69dfc05e#body_text
is schema:about of	named entity 'SEWAGE' named entity 'metagenomics' named entity 'field' named entity 'DNA' named entity 'human waste' named entity 'sequencing' named entity 'wide range' named entity 'viral' named entity 'Environmental' named entity 'precipitation' named entity 'flocculation' named entity 'mixed' named entity 'virus' named entity 'KIT' covid:arg/3b5ea760c63aaff964de32541643d92c69dfc05e named entity 'HAVE' named entity 'UNDERSTANDING' named entity 'THESE' named entity 'ALLOW' named entity 'SIGNIFICANT' named entity 'USED' named entity 'PRECIPITATION' named entity 'RNA' named entity 'DIFFICULT' named entity 'CHALLENGES' named entity 'RANGE' named entity 'FILTRATION' named entity 'PROTOCOLS' named entity 'POLYETHYLENE GLYCOL' named entity 'SEWAGE' named entity 'NOVEL' named entity 'VIRAL PATHOGENS' named entity 'DIVERSITY' named entity 'STRUCTURES' named entity 'METAGENOMICS' named entity 'FIELD' named entity 'FOUND' named entity 'FLOCCULATION' named entity 'EVALUATE' named entity 'CONCENTRATED' named entity 'HOUSEHOLD' named entity 'RAW' named entity 'HUMAN' named entity 'STUDY' named entity 'METAGENOMIC SEQUENCING' named entity 'DETECTED' named entity 'CONTRIBUTE ' named entity 'MINI' named entity 'TREATMENT EFFICIENCY' named entity 'METHODS' named entity 'ENVIRONMENTAL' named entity 'WASTE WATER TREATMENT' named entity 'CURRENT' named entity 'SKIM MILK' named entity 'CONCENTRATION' named entity 'INDUSTRIAL' named entity 'EVALUATION' named entity 'EXTRACTED' named entity 'DETECTION' named entity 'GENOME' named entity 'MIXED' named entity 'HARBOR' named entity 'DEVELOPMENT' named entity 'SAMPLE' named entity 'SAMPLES' named entity 'LOW' named entity 'WIDE' named entity 'SURVEILLANCE' named entity 'GENOMIC'

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