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

• DOI: 10.1021/acs.jproteome.0c00887
• Publication Date: 2021-01-26T21:27:40Z
• Authors: Justyna Saadi; Saoussen Oueslati; Laurent Bellanger; Fabrice Gallais; Laurent Dortet; Anne-Marie Roque-...; Christophe Junot; Thierry Naas; François Fenaille; François Becher
• Keywords: Proteomics; 0301 basic medicine; Physiology; [SDV]Life Sciences [q-bio]; [SDV.BBM]Life Sciences [q-bio]/Biochemistry; SARS-CoV -2 detection; Peptide Atlas; Biochemistry; Absolute quantification; nasopharyngeal swabs; PASSEL; Quantitative Assessment; Tandem Mass Spectrometry; Nasopharynx; 30 pfu; Nasopharyngeal Swabs Stored; Spike Proteins; Cancer; mass spectrometry; targeted; RT-PCR detection threshold; evaluation; immunoassay dipsticks; protein content; pellet digestion protocol; VTM-stored nasopharyngeal; SARS-CoV -2; 3. Good health; Infectious Diseases; data; Spike Glycoprotein, Coronavirus; method; Biotechnology; Biological Sciences not elsewhere classified; control patients; COVID -19; 570; Chemical Sciences not elsewhere classified; transport media; first-line diagnosis; Immunology; Biophysics; 610; mass spectrometry assay; virus; Transport Medium; Sensitivity and Specificity; Specimen Handling; mass spectrometry detection; Viral Proteins; 03 medical and health sciences; isotope-labeled versions; Virology; 616; [CHIM]Chemical Sciences; Humans; S proteins; [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology; Nucleocapsid; Molecular Biology; SARS-CoV -2 antigen assay; SARS-CoV-2; COVID-19; Reproducibility of Results; General Chemistry; sensitivity; PASS; sample; quantification; laboratory reagents; LC-MS; Culture Media; constitutive peptides representative; Chromatography, Liquid

Alternative methods to RT-PCR for SARS-CoV-2 detection are investigated 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 in nasopharyngeal swab samples using common laboratory reagents. The method employs high sensitivity and selectivity targeted detection, monitoring nine constitutive peptides representative three main proteins straightforward pellet digestion protocol convenient routine applications. Absolute quantification N, M, S was achieved by addition isotope-labeled versions best peptides. Limit recovery, precision, linearity were thoroughly evaluated four transport media (VTM) containing distinct total protein content. sensitive all with limit determined at 2 × 103 pfu/mL, corresponding as low 30 pfu injected into LC-MS/MS system. When tested VTM-stored from positive control patients, similar better than rapid immunoassay dipsticks, revealing threshold Ct ∼ 24. study represents first thorough evaluation robustness nasal swabs, constituting promising antigen first-line diagnosis COVID-19 compatible constraints clinical settings. raw files generated this can be found PASSEL (Peptide Atlas) under set identifier PASS01646.