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Article

Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses

1
Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
2
CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
3
Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
4
Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France
5
Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France
6
PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France
7
European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(10), 1539; https://doi.org/10.3390/microorganisms8101539
Received: 22 September 2020 / Revised: 3 October 2020 / Accepted: 5 October 2020 / Published: 6 October 2020
(This article belongs to the Special Issue Respiratory Viruses in the Age of Metagenomics)
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization. View Full-Text
Keywords: viral metagenomics; next-generation sequencing; acid nucleic extraction; sample cross-contamination; kitome viral metagenomics; next-generation sequencing; acid nucleic extraction; sample cross-contamination; kitome
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MDPI and ACS Style

Sabatier, M.; Bal, A.; Destras, G.; Regue, H.; Quéromès, G.; Cheynet, V.; Lina, B.; Bardel, C.; Brengel-Pesce, K.; Navratil, V.; Josset, L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020, 8, 1539. https://doi.org/10.3390/microorganisms8101539

AMA Style

Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms. 2020; 8(10):1539. https://doi.org/10.3390/microorganisms8101539

Chicago/Turabian Style

Sabatier, Marina, Antonin Bal, Grégory Destras, Hadrien Regue, Grégory Quéromès, Valérie Cheynet, Bruno Lina, Claire Bardel, Karen Brengel-Pesce, Vincent Navratil, and Laurence Josset. 2020. "Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses" Microorganisms 8, no. 10: 1539. https://doi.org/10.3390/microorganisms8101539

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