Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

  1. Daniel Blanco-Melo
  2. Benjamin E. Nilsson-Payant
  3. Wen-Chun Liu
  4. Skyler Uhl
  5. Daisy Hoagland
  6. Rasmus Møller
  7. Tristan X. Jordan
  8. Kohei Oishi
  9. Maryline Panis
  10. David Sachs
  11. Taia T. Wang
  12. Robert E. Schwartz
  13. Jean K. Lim
  14. Randy A. Albrecht
  15. Benjamin R. tenOever

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.03.24.004655: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableNormal human bronchial epithelial (NHBE) cells (Lonza, CC-2540 Lot# 580580) were isolated from a 79-year-old Caucasian female and were maintained in bronchial epithelial growth media (Lonza, CC-3171) supplemented with BEGM SingleQuots as per the manufacturer’s instructions (Lonza, CC-4175) at 37°C and 5% CO2.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cell Culture: Human adenocarcinomic alveolar basal epithelial (A549) cells (ATCC, CCL-185), Madin-Darby Canine Kidney (MDCK) cells (ATCC, CCL-34), African green monkey kidney epithelical Vero E6 cells (ATCC, CRL-1586) and African green monkey kidney epithelical BS-C-1 cells (ATCC, CCL-26) were maintained at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Corning).
    A549
    suggested: None
    MDCK
    suggested: None
    BS-C-1
    suggested: None
    Recombinant GFP-expressing human respiratory syncytial virus, strain A2 (rgRSV[224]) was generously provided by Dr. M. Peeples (OSU) and was described previously12. rgRSV[224] was grown in BSC-1 cells in in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose and 4 mM L-glutamine.
    BSC-1
    suggested: ATCC Cat# CCL-26, RRID:CVCL_0607)
    SARS-CoV-2 was propagated in Vero E6 cells in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Gene set enrichment analysis (GSEA) was performed on gene expression profiles from mock and SARS-CoV-2 treated cells comparing to a composite list of genes involved in Type-I IFN response (GO:0035457, GO:0035458, GO:0035455, GO:0035456, GO:0034340, and HALLMARK_INTERFERON_ALPHA_RESPONSE)16.
    Gene set enrichment analysis
    suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
    Alignments to viral genomes was performed using bowtie2.
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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 10.1016/j.cell.2020.04.026
  3. Version published to 10.1101/2020.03.24.004655v1 on bioRxiv