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

eLife

Jessica J Alm¹  Lars Engstrand²  Terry W Pearson³  Morteza Razavi³  Matthew E Pope³  Leigh N Andersson³  Richard Yip³  Andreas Hober⁴  Fredrik Edfors⁵  Mathias Uhlén⁵  Khue Hua Tran-Minh⁵  Johannes PC Vissers⁶  Samantha Ferries⁶  Lisa Calton⁶  Dominic Foley⁶  Rebecca Pattison⁶  Amy Bartlett⁶  Sigurd Hermansson⁶  Thomas McDonald⁶  Ingvar Betner⁶ 

[1] Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska Institutet, Solna, Sweden;Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden;SISCAPA Assay Technologies, Inc, Victoria, Canada;Science for Life Laboratory, Solna, Sweden;Science for Life Laboratory, Solna, Sweden;The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm, Sweden;Waters Corporation, Milford, United Kingdom;

关键词: SARS CoV-2;    COVID-19;    SISCAPA;    proteomics;    diagnostics;    mass spectrometry;    Human;   

DOI  :  10.7554/eLife.70843

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY