Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
Highlights
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease
Data-dependent acquisition (DDA) analyses revealed the presence of 119 unique peptides from eight proteins out of the 14 proteins predicted by UniProt SARS-CoV-2 (Table 1)
In response to the urgent need to develop alternative diagnostic tests for the novel coronavirus (SARS-CoV-2) pandemic, we developed a method that satisfies the following requirements: specificity towards SARS-CoV-2; good sensitivity compared to the gold standard real-time RT-PCR; sample preparation of highvolume processing in the shortest time possible; and fast acquisition by multiplexing liquid chromatography coupled to tandem Mass spectrometry (MS)
Summary
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. Serologic immunoassays targeting IgA, IgM, or IgG provide historic information about viral exposure, but their sensitivity in the acute phase of SARS-CoV-2 infections is still not well established[6]. They often suffer from interference because antibody recognition is not free of error and may be confounded by the presence of other molecules
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