Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis

Author:

Hober Andreas1ORCID,Tran-Minh Khue Hua12,Foley Dominic3,McDonald Thomas3,Vissers Johannes PC3,Pattison Rebecca3,Ferries Samantha3,Hermansson Sigurd3,Betner Ingvar3,Uhlén Mathias12,Razavi Morteza4,Yip Richard4,Pope Matthew E4,Pearson Terry W4,Andersson Leigh N4,Bartlett Amy3,Calton Lisa3,Alm Jessica J5,Engstrand Lars6,Edfors Fredrik12ORCID

Affiliation:

1. Science for Life Laboratory

2. The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health

3. Waters Corporation

4. SISCAPA Assay Technologies, Inc

5. Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska Institutet

6. Microbiology, Tumour and Cell Biology, Karolinska Institutet

Abstract

Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity 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 phosphate-buffered saline (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 correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out 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% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct ≤ 30). 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.

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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