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

  1. Andreas Hober
  2. Khue Hua Tran-Minh
  3. Dominic Foley
  4. Thomas McDonald
  5. Johannes PC Vissers
  6. Rebecca Pattison
  7. Samantha Ferries
  8. Sigurd Hermansson
  9. Ingvar Betner
  10. Mathias Uhlén
  11. Morteza Razavi
  12. Richard Yip
  13. Matthew E Pope
  14. Terry W Pearson
  15. Leigh N Andersson
  16. Amy Bartlett
  17. Lisa Calton
  18. Jessica J Alm
  19. Lars Engstrand
  20. Fredrik Edfors  Is a corresponding author
  1. Science for Life Laboratory, Sweden
  2. Royal Institute of Technology, Sweden
  3. Waters Corporation, United Kingdom
  4. Waters Corporation, Sweden
  5. KTH Royal Institute of Technology, Sweden
  6. SISCAPA Assay Technologies, Inc, United States
  7. Karolinska Institutet, Sweden

Abstract

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.<br />The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their corresponding RT-PCR readout (r=0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a 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% 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.

Data availability

The ProteomeXchange ID for this dataset is PXD026366. The proteomics data have been deposited to Panorama Public (https://panoramaweb.org/sars-cov-2_siscapa.url; allowing for access to raw files and integrated peak areas from as well as visualization of all LC-MRM/MS chromatograms.

The following data sets were generated

Article and author information

Author details

  1. Andreas Hober

    Science for Life Laboratory, Solna, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8947-2562
  2. Khue Hua Tran-Minh

    Royal Institute of Technology, Solna, Sweden
    Competing interests
    No competing interests declared.
  3. Dominic Foley

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Dominic Foley, employed by Waters Corporation.
  4. Thomas McDonald

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Thomas McDonald, employed by Waters Corporation.
  5. Johannes PC Vissers

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Johannes PC Vissers, employed by Waters Corporation.
  6. Rebecca Pattison

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Rebecca Pattison, employed by Waters Corporation.
  7. Samantha Ferries

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Samantha Ferries, employed by Waters Corporation.
  8. Sigurd Hermansson

    Waters Corporation, Stockholm, Sweden, Sweden
    Competing interests
    Sigurd Hermansson, employed by Waters Corporation.
  9. Ingvar Betner

    Waters Corporation, Stockholm, Sweden, Sweden
    Competing interests
    Ingvar Betner, employed by Waters Corporation.
  10. Mathias Uhlén

    Systems Biology, KTH Royal Institute of Technology, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  11. Morteza Razavi

    SISCAPA Assay Technologies, Inc, Washington, United States
    Competing interests
    Morteza Razavi, employed by SISCAPA Assay Technologies.
  12. Richard Yip

    SISCAPA Assay Technologies, Inc, Washington, United States
    Competing interests
    Richard Yip, employed by SISCAPA Assay Technologies.
  13. Matthew E Pope

    SISCAPA Assay Technologies, Inc, Washington, United States
    Competing interests
    Matthew E Pope, employed by SISCAPA Assay Technologies.
  14. Terry W Pearson

    SISCAPA Assay Technologies, Inc, Washington, United States
    Competing interests
    Terry W Pearson, employed by SISCAPA Assay Technologies.
  15. Leigh N Andersson

    SISCAPA Assay Technologies, Inc, Washington, United States
    Competing interests
    Leigh N Andersson, employed by SISCAPA Assay Technologies.
  16. Amy Bartlett

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Amy Bartlett, employed by Waters Corporation.
  17. Lisa Calton

    Waters Corporation, Milford, United Kingdom
    Competing interests
    Lisa Calton, employed by Waters Corporation.
  18. Jessica J Alm

    Karolinska Institutet, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  19. Lars Engstrand

    Karolinska Institutet, Stockholm, Sweden
    Competing interests
    No competing interests declared.
  20. Fredrik Edfors

    Royal Institute of Technology, Solna, Sweden
    For correspondence
    fredrik.edfors@scilifelab.se
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0017-7987

Funding

No external funding was received for this work.

Ethics

Human subjects: The study was performed in accordance with the declaration of Helsinki and the study protocol ("Jämförande studier av Covid-19 smitta och antikroppssvar i olika grupper i samhället") was approved by the Ethical Review Board of Linköping, Sweden (Regionala etikprövningsnämnden, Linköping, DNR - 2020-06395). Informed consent and consent to publish, including consent to publish anonymized data, was obtained from all subjects.

Reviewing Editor

  1. Maarten Dhaenens, ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium

Publication history

  1. Received: May 31, 2021
  2. Preprint posted: June 4, 2021 (view preprint)
  3. Accepted: November 4, 2021
  4. Accepted Manuscript published: November 8, 2021 (version 1)
  5. Version of Record published: November 26, 2021 (version 2)

Copyright

© 2021, Hober et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Andreas Hober
  2. Khue Hua Tran-Minh
  3. Dominic Foley
  4. Thomas McDonald
  5. Johannes PC Vissers
  6. Rebecca Pattison
  7. Samantha Ferries
  8. Sigurd Hermansson
  9. Ingvar Betner
  10. Mathias Uhlén
  11. Morteza Razavi
  12. Richard Yip
  13. Matthew E Pope
  14. Terry W Pearson
  15. Leigh N Andersson
  16. Amy Bartlett
  17. Lisa Calton
  18. Jessica J Alm
  19. Lars Engstrand
  20. Fredrik Edfors
(2021)
Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis
eLife 10:e70843.
https://doi.org/10.7554/eLife.70843
  1. Further reading

Further reading

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