Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison

  1. Ioanna-Evdokia Galani
  2. Nikoletta Rovina
  3. Vicky Lampropoulou
  4. Vasiliki Triantafyllia
  5. Maria Manioudaki
  6. Eleftherios Pavlos
  7. Evangelia Koukaki
  8. Paraskevi C. Fragkou
  9. Vasiliki Panou
  10. Vasiliki Rapti
  11. Ourania Koltsida
  12. Andreas Mentis
  13. Nikolaos Koulouris
  14. Sotirios Tsiodras
  15. Antonia Koutsoukou
  16. Evangelos Andreakos

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.08.21.20179291: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study conforms to the principles outlined in the Declaration of Helsinki, and received approval by the Ethics Committees of the “Sotiria” General Chest Diseases Hospital, Athens,
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, raw reads were pre-processed using FastQC v.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    0.11.2 and cutadapt v.1.6, and then mapped to the human genome (GRCh38) using the TopHat version 2.0.13, Bowtie v.
    TopHat
    suggested: (TopHat, RRID:SCR_013035)
    Bowtie
    suggested: (Bowtie, RRID:SCR_005476)
    1.1.1 and Samtools version v.1.1.
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The read count table was produced using HTSeq v.0.6.
    HTSeq
    suggested: (HTSeq, RRID:SCR_005514)
    Following filtering of raw read counts with a threshold of 10 in at least one dataset, resulting in a total of 21880 genes, DESeq2 analysis was performed36.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    Pathway enrichment analysis was conducted using ClueGO and CluePedia plugin of Cytoscape.
    ClueGO
    suggested: (ClueGO, RRID:SCR_005748)
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    Clustering and dendrograms were performed with hclust function and ggdendro package, respectively, in R.
    hclust
    suggested: (HCLUST, RRID:SCR_009154)
    Data and software availability: The raw RNAseq data have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) under BioProject accession number # PRJNA638753.
    http://www.ncbi.nlm.nih.gov/geo/
    suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Statistical analysis: Data were analyzed on GraphPad Prism software.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Polar charts from the ggplot2 R package were used for the visualization of the differences in cytokine response patterns.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    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 10.1038/s41590-020-00840-x
  3. Version published to 10.1101/2020.08.21.20179291v1 on medRxiv