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Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
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 concentratio...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242460/ https://www.ncbi.nlm.nih.gov/pubmed/28099518 http://dx.doi.org/10.1371/journal.pone.0170199 |
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author | Hjelmsø, Mathis Hjort Hellmér, Maria Fernandez-Cassi, Xavier Timoneda, Natàlia Lukjancenko, Oksana Seidel, Michael Elsässer, Dennis Aarestrup, Frank M. Löfström, Charlotta Bofill-Mas, Sílvia Abril, Josep F. Girones, Rosina Schultz, Anna Charlotte |
author_facet | Hjelmsø, Mathis Hjort Hellmér, Maria Fernandez-Cassi, Xavier Timoneda, Natàlia Lukjancenko, Oksana Seidel, Michael Elsässer, Dennis Aarestrup, Frank M. Löfström, Charlotta Bofill-Mas, Sílvia Abril, Josep F. Girones, Rosina Schultz, Anna Charlotte |
author_sort | Hjelmsø, Mathis Hjort |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5242460 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-52424602017-02-06 Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing Hjelmsø, Mathis Hjort Hellmér, Maria Fernandez-Cassi, Xavier Timoneda, Natàlia Lukjancenko, Oksana Seidel, Michael Elsässer, Dennis Aarestrup, Frank M. Löfström, Charlotta Bofill-Mas, Sílvia Abril, Josep F. Girones, Rosina Schultz, Anna Charlotte PLoS One Research Article 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. Public Library of Science 2017-01-18 /pmc/articles/PMC5242460/ /pubmed/28099518 http://dx.doi.org/10.1371/journal.pone.0170199 Text en © 2017 Hjelmsø et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Hjelmsø, Mathis Hjort Hellmér, Maria Fernandez-Cassi, Xavier Timoneda, Natàlia Lukjancenko, Oksana Seidel, Michael Elsässer, Dennis Aarestrup, Frank M. Löfström, Charlotta Bofill-Mas, Sílvia Abril, Josep F. Girones, Rosina Schultz, Anna Charlotte Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title | Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title_full | Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title_fullStr | Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title_full_unstemmed | Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title_short | Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing |
title_sort | evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242460/ https://www.ncbi.nlm.nih.gov/pubmed/28099518 http://dx.doi.org/10.1371/journal.pone.0170199 |
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