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We evaluated the diagnostic performance of 4 commercially NAAT for detecting SARS-CoV-2 RNA, Influenza type A/B virus and RSV. Included tests were the Allplex™ SARS-CoV-2 fast PCR Assay (RNA extraction-free), Allplex™ RV Master Assay, Allplex™ SARS-CoV-2 fast MDx Assay (LAMP) and Aptima™ SARS-CoV-2/Flu Assay (RT-TMA). The assays' performance characteristics were determined using nasopharyngeal swabs from 270 patients with suspected SARS-CoV-2 infection. A total of 215 SARS-CoV-2 positive, 55 negative nasopharyngeal swabs and 19 bacteria strains were included. The sensitivities and specificities for detecting SARS-CoV-2, Influenza type A virus and RSV ranged between 81.8% and 100% with extremely good agreements (κ ≥ 86.8 %). The Aptima™ SARS-CoV-2/Flu Assay introduced a new result parameter, that is, TTime. Here, we showed that TTime may be used as a surrogate for Ct-value. We concluded that all assays assessed in this study can be used for routine detection of SARS-CoV-2, Influenza type A virus and RSV., Competing Interests: Declaration of Competing Interest The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics., Competing Interests: The authors have declared that no competing interests exist.