Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing

Research output: Contribution to journalJournal article – Annual report year: 2017Researchpeer-review

Standard

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, Natalie; Lukjancenko, Oksana; Seidel, Michael; Elsasser, Dennis; Aarestrup, Frank Møller; Löfström, Charlotta; Bofill-Mas, Silvia; Abril, Josep F.; Girones, Rosina; Schultz, Anna Charlotte.

In: PLOS ONE, Vol. 12, No. 1, e0170199, 2017.

Research output: Contribution to journalJournal article – Annual report year: 2017Researchpeer-review

Harvard

APA

CBE

MLA

Vancouver

Author

Bibtex

@article{feb45497ce2d4552a4e77f1f217e416b,
title = "Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing",
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{\^A}{\circledR} miniMAG{\^A}{\circledR}, or PowerViral{\^A}{\circledR} 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{\^A}{\circledR} 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.",
keywords = "Medicine (all), Biochemistry, Genetics and Molecular Biology (all), Agricultural and Biological Sciences (all)",
author = "Hjelms{\o}, {Mathis Hjort} and Maria Hellm{\'e}r and Xavier Fernandez-Cassi and Natalie Timoneda and Oksana Lukjancenko and Michael Seidel and Dennis Elsasser and Aarestrup, {Frank M{\o}ller} and Charlotta L{\"o}fstr{\"o}m and Silvia Bofill-Mas and Abril, {Josep F.} and Rosina Girones and Schultz, {Anna Charlotte}",
year = "2017",
doi = "10.1371/journal.pone.0170199",
language = "English",
volume = "12",
journal = "P L o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "1",

}

RIS

TY - JOUR

T1 - Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing

AU - Hjelmsø, Mathis Hjort

AU - Hellmér, Maria

AU - Fernandez-Cassi, Xavier

AU - Timoneda, Natalie

AU - Lukjancenko, Oksana

AU - Seidel, Michael

AU - Elsasser, Dennis

AU - Aarestrup, Frank Møller

AU - Löfström, Charlotta

AU - Bofill-Mas, Silvia

AU - Abril, Josep F.

AU - Girones, Rosina

AU - Schultz, Anna Charlotte

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - Medicine (all)

KW - Biochemistry, Genetics and Molecular Biology (all)

KW - Agricultural and Biological Sciences (all)

U2 - 10.1371/journal.pone.0170199

DO - 10.1371/journal.pone.0170199

M3 - Journal article

VL - 12

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 1

M1 - e0170199

ER -