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Saadi J, Oueslati S, Bellanger L, Gallais F, Dortet L, Roque-Afonso AM, Junot C, Naas T, Fenaille F, Becher F. 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. J Proteome Res 2021; 20:1434-1443. [PMID: 33497234 DOI: 10.1021/acs.jproteome.0c00887] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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Affiliation(s)
- Justyna Saadi
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Saoussen Oueslati
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Laurent Bellanger
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Laurent Dortet
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Anne-Marie Roque-Afonso
- Service de Virologie, Hôpital Paul-Brousse, APHP Paris Saclay, and UMR 1193 Physiopathogénèse et Traitement des Maladies du Foie, 94800 Villejuif, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Thierry Naas
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - François Becher
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
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Saleh S, Staes A, Deborggraeve S, Gevaert K. Targeted Proteomics for Studying Pathogenic Bacteria. Proteomics 2019; 19:e1800435. [DOI: 10.1002/pmic.201800435] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Sara Saleh
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - An Staes
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - Stijn Deborggraeve
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
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Rifflet A, Filali S, Chenau J, Simon S, Fenaille F, Junot C, Carniel E, Becher F. Quantification of low abundance Yersinia pestis markers in dried blood spots by immuno-capture and quantitative high-resolution targeted mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:268-277. [PMID: 31096787 DOI: 10.1177/1469066718795978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plague, caused by the bacterium Yersinia pestis, is still present in several countries worldwide. Besides, Y. pestis has been designated as Tier 1 agent, the highest rank of bioterrorism agents. In this context, reliable diagnostic methods are of great importance. Here, we have developed an original workflow based upon dried blood spot for simplified sampling of clinical specimens, and specific immuno-mass spectrometry monitoring of Y. pestis biomarkers. Targeted proteins were selectively enriched from dried blood spot extracts by multiplex immunocapture using antibody-coated magnetic beads. After accelerated on-beads digestion, proteotypic peptides were monitored by multiplex LC-MS/MS through the parallel reaction monitoring mode. The DBS-IC-MS assay was designed to quantify both F1 and LcrV antigens, although 10-fold lower sensitivity was observed with LcrV. The assay was successfully validated for F1 with a lower limit of quantification at 5 ng·mL-1 in spiked blood, corresponding to only 0.1 ng on spots. In vivo quantification of F1 in blood and organ samples was demonstrated in the mouse model of pneumonic plague. The new assay could help to simplify the laboratory confirmation of positive point of care F1 dipstick.
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Affiliation(s)
- Aline Rifflet
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Sofia Filali
- 2 Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Jérôme Chenau
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Stéphanie Simon
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - François Fenaille
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Christophe Junot
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | | | - François Becher
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
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