A common TMPRSS2 variant has a protective effect against severe COVID-19

  1. Alessia David
  2. Nicholas Parkinson
  3. Thomas P Peacock
  4. Erola Pairo-Castineira
  5. Tarun Khanna
  6. Aurelie Cobat
  7. Albert Tenesa
  8. Vanessa Sancho-Shimizu
  9. Jean-Laurent Casanova
  10. Laurent Abel
  11. Wendy S. Barclay
  12. J.Kenneth Baillie
  13. Michael JE Sternberg

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Abstract

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  1. Version published to 10.1016/j.retram.2022.103333
  2. ScreenIT

    SciScore for 10.1101/2021.03.04.21252931: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    Near infra-red (NIR) secondary antibodies, IRDye® 680RD Goat anti-mouse (abcam; ab216776) and IRDye® 800CW Goat anti-rabbit (abcam; ab216773) were subsequently used.
    anti-mouse
    suggested: None
    anti-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Participants: Genetics Of Mortality In Critical Care (GenOMICC) and the International Severe Acute Respiratory Infection Consortium (ISARIC) Coronavirus Clinical Characterisation Consortium (4C) (ISARIC 4C) Cells, pseudovir us and plasmid: Human embryonic kidney 293T cells (293Ts; ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM), 10% foetal calf serum (FCS), 1% non-essential amino acids (NEAA), 1% penicillin-streptomycin (P/S) at 37°C, 5% CO2.
    293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Given the similarity of the Phyre and the SWISS-MODEL 3D models assessed using the root mean square deviation (RMSD) (Phyre versus SWISS-MODEL model=0.30Å RMSD), all subsequent analyses should not be sensitive to which model is selected.
    Phyre
    suggested: (Phyre, RRID:SCR_010270)
    In addition, we used the SIFT 48 and Polyphen2 49 variant predictors, which mainly use evolutionary conservation to assess the effect of each variant.
    SIFT
    suggested: (SIFT, RRID:SCR_012813)
    Polyphen2
    suggested: None
    CONDEL 50, which reports a weighted average of the scores from fatHMM and MutationAssessor, and ii.
    MutationAssessor
    suggested: (MutationAssessor, RRID:SCR_005762)
    Densitometry was performed using ImageJ.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    Trans-ethnic meta-analysis of GenOMICC data for different ancestries was performed by METAL using an inverse-variance weighted method and the P-value for heterogeneity was calculated with Cochran’s Q-test for heterogeneity implemented in the same software 54.
    METAL
    suggested: (METAL, RRID:SCR_002013)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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.

  3. Version published to 10.1101/2021.03.04.21252931v1 on medRxiv