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Quantitative Assessment of SARS-CoV-2 Virus in Nasopharyngeal Swabs Stored in Transport Medium by a Straightforward LC-MS/MS Assay Targeting Nucleocapsid, Membrane, and Spike Proteins.
Saadi, Justyna; Oueslati, Saoussen; Bellanger, Laurent; Gallais, Fabrice; Dortet, Laurent; Roque-Afonso, Anne-Marie; Junot, Christophe; Naas, Thierry; Fenaille, François; Becher, François.
  • Saadi J; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France.
  • Oueslati S; Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France.
  • Bellanger L; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France.
  • Gallais F; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France.
  • Dortet L; Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France.
  • Roque-Afonso AM; Service de Virologie, Hôpital Paul-Brousse, APHP Paris Saclay, and UMR 1193 Physiopathogénèse et Traitement des Maladies du Foie, 94800 Villejuif, France.
  • Junot C; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France.
  • Naas T; Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France.
  • Fenaille F; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France.
  • Becher F; Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France.
J Proteome Res ; 20(2): 1434-1443, 2021 02 05.
Article in English | MEDLINE | ID: covidwho-1065788
ABSTRACT
Alternative methods to RT-PCR for SARS-CoV-2 detection are investigated to provide complementary data on viral proteins, increase the number of tests performed, or identify false positive/negative results. Here, we have developed a simple mass spectrometry assay for SARS-CoV-2 in nasopharyngeal swab samples using common laboratory reagents. The method employs high sensitivity and selectivity targeted mass spectrometry detection, monitoring nine constitutive peptides representative of the three main viral proteins and a straightforward pellet digestion protocol for convenient routine applications. Absolute quantification of N, M, and S proteins was achieved by addition of isotope-labeled versions of best peptides. Limit of detection, recovery, precision, and linearity were thoroughly evaluated in four representative viral transport media (VTM) containing distinct total protein content. The protocol was sensitive in all swab media with limit of detection determined at 2 × 103 pfu/mL, corresponding to as low as 30 pfu injected into the LC-MS/MS system. When tested on VTM-stored nasopharyngeal swab samples from positive and control patients, sensitivity was similar to or better than rapid immunoassay dipsticks, revealing a corresponding RT-PCR detection threshold at Ct ∼ 24. The study represents the first thorough evaluation of sensitivity and robustness of targeted mass spectrometry in nasal swabs, constituting a promising SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 and compatible with the constraints of clinical settings. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01646.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Nasopharynx / Chromatography, Liquid / Tandem Mass Spectrometry / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2021 Document Type: Article Affiliation country: Acs.jproteome.0c00887

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Nasopharynx / Chromatography, Liquid / Tandem Mass Spectrometry / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2021 Document Type: Article Affiliation country: Acs.jproteome.0c00887