Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window

  1. Duarte Gouveia
  2. Guylaine Miotello
  3. Fabrice Gallais
  4. Jean-Charles Gaillard
  5. Stéphanie Debroas
  6. Laurent Bellanger
  7. Jean-Philippe Lavigne
  8. Albert Sotto
  9. Lucia Grenga
  10. Olivier Pible
  11. Jean Armengaud

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Abstract

Rapid but yet sensitive, specific and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostic that would not require specific reagents are worth to investigate not only for fighting the COVID-19 pandemic, but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.19.161000: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the institutional review boards of the University Hospital of Nîmes, France (2020-05-01).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Infection and virus purification: Vero E6 cells (1×106) seeded into 150 cm2 flasks were grown to cell confluence in 15 ml DMEM supplemented with 5% FCS and 0.5% penicillin–streptomycin for one night at 37°C under 9% CO2.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    MS/MS spectra from the simili SARS-CoV-2 contaminated swabs and from the COVID-19 nasopharyngeal swabs were assigned with the MASCOT Daemon 2.3.2 search engine
    MASCOT Daemon
    suggested: None
    MS1 peak areas were evaluated with Skyline (27).
    Skyline
    suggested: (Skyline, RRID:SCR_014080)
    Briefly, we created spectral libraries based on the DAT files from each MASCOT search (cut-of 0.99) and uploaded the MS1 full scan information contained in the raw files.
    MASCOT
    suggested: (Mascot, RRID:SCR_014322)
    Mass spectrometry and proteomics data: The mass spectrometry and proteomics data acquired on simili swabs have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (28) with the dataset identifiers PXD019686 and 10.6019/PXD019686.
    PRIDE
    suggested: (Pride-asap, RRID:SCR_012052)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.06.19.161000 on bioRxiv