COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

  1. Reina S Sikkema
  2. Suzan D Pas
  3. David F Nieuwenhuijse
  4. Áine O'Toole
  5. Jaco Verweij
  6. Anne van der Linden
  7. Irina Chestakova
  8. Claudia Schapendonk
  9. Mark Pronk
  10. Pascal Lexmond
  11. Theo Bestebroer
  12. Ronald J Overmars
  13. Stefan van Nieuwkoop
  14. Wouter van den Bijllaardt
  15. Robbert G Bentvelsen
  16. Miranda M L van Rijen
  17. Anton G M Buiting
  18. Anne J G van Oudheusden
  19. Bram M Diederen
  20. Anneke M C Bergmans
  21. Annemiek van der Eijk
  22. Richard Molenkamp
  23. Andrew Rambaut
  24. Aura Timen
  25. Jan A J W Kluytmans
  26. Bas B Oude Munnink
  27. Marjolein F Q Kluytmans van den Bergh
  28. Marion P G Koopmans

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Abstract

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  1. Version published to 10.1016/s1473-3099(20)30527-2
  2. ScreenIT

    SciScore for 10.1101/2020.04.26.20079418: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical approval was obtained from the Ethics Committee Brabant, with a waiver of written informed consent (METC Brabant/20.134/NW2020–26).
    Consent: Verbal informed consent was obtained from all HCWs for SARS-CoV-2 testing, sequencing and data collection.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The consensus genome was extracted and positions with a coverage <30 were replaced with an “N” with a custom script using biopython and pysam, as previously described12.
    biopython
    suggested: (Biopython, RRID:SCR_007173)
    The alignment was manually inspected and trimmed of the 5’ and 3’ UTRs in Geneious v11.1.3 (geneious.com) to include only coding regions.
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    Bayesian phylogenetic trees were estimated using BEAST v1.10.422 using an HKY nucleotide subsititution model23 and a strict molecular clock.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The maximum clade credibility (MCC) tree was inferred using TreeAnnotator and visualized using baltic (https://github.com/evogytis/baltic) and custom python scripts.
    python
    suggested: (IPython, RRID:SCR_001658)
    All analyses were performed with SPSS version 25.0 (IBM, Armonk, NY, USA).
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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 10.1101/2020.04.26.20079418v1 on medRxiv