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Article Dans Une Revue Microorganisms Année : 2020

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

Marina Sabatier
  • Fonction : Auteur
Antonin Bal
Grégory Destras
  • Fonction : Auteur
Hadrien Regue
  • Fonction : Auteur
Grégory Quéromès
Valérie Cheynet
  • Fonction : Auteur
Bruno Lina
Karen Brengel-Pesce
  • Fonction : Auteur
Vincent Navratil
  • Fonction : Auteur
Laurence Josset

Résumé

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.

Dates et versions

hal-04383021 , version 1 (09-01-2024)

Identifiants

Citer

Marina Sabatier, Antonin Bal, Grégory Destras, Hadrien Regue, Grégory Quéromès, et al.. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms, 2020, 8 (10), pp.1539. ⟨10.3390/microorganisms8101539⟩. ⟨hal-04383021⟩
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