Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment LC-MS/MS Analysis

Hober, A.; Hua, T.-M. K.; Foley, D.; McDonald, T.; Vissers, J. P. C.; Pattison, R.; Ferries, S.; Hermansson, S.; Betner, I.; Uhlen, M.; Razavi, M.; Yip, R.; Pope, M. E.; Pearson, T. W.; Anderson, N. L.; Bartlett, A.; Carlton, L.; Alm, J. J.; Engstrand, L.; Edfors, F.

Reliable, robust, large-scale molecular testing for SARS-CoV-2 is essential for monitoring the ongoing Covid-19 pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immunoaffinity enrichment combined with liquid chromatography - mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in PBS swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their corresponding RT-PCR readout. The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with quantitative readout of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% estimated specificity and 83.3% estimated sensitivity when analyzing clinical samples collected from asymptomatic individuals. These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.