Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

  1. Yu-Sheng Chen
  2. Shuaiyao Lu
  3. Bing Zhang
  4. Tingfu Du
  5. Wen-Jie Li
  6. Meng Lei
  7. Yanan Zhou
  8. Yong Zhang
  9. Penghui Liu
  10. Yong-Qiao Sun
  11. Yong-Liang Zhao
  12. Ying Yang
  13. Xiaozhong Peng
  14. Yun-Gui Yang

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Abstract

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  1. Version published to 10.1007/s13238-021-00861-8
  2. ScreenIT

    SciScore for 10.1101/2021.06.06.447293: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    S1 to S11 Tables S1 to S6 Cell culture and virus infection: HEK293T (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences,
    HEK293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    3111C0001CCC000091), Huh-7 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000679), Calu-3 (Cell Resource Center, Institute of Basic Medicine Chinese Academy of Medical Sciences, 3111C0001CCC000032), Cos-7 (Kunming Cell Bank, Chinese Academy of Sciences, 3153C0001000000037) and MA-104 (Chinese Typical Culture Preservation Center Cell Bank, 3142C0001000000041) cells were cultured in DMEM (ThermoFisher,0030034DJ) supplemented with 10% fetal bovine serum (Gibco, 10099-141C) and penicillin-streptomycin (ThermoFisher,15140122) at 37°C, 5% CO2.
    Huh-7
    suggested: None
    Software and Algorithms
    SentencesResources
    Bioinformatics analysis of whole genome sequencing data: Reads from whole genome sequencing data were mapped to human genome plus SARS-CoV-2 genome by using BWA (version 0.7.17)3, and genome coverage statistics was obtained by samtools (version 1.12)4.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Chimeric gene analysis: Chimeric reads between host and SARS-CoV-2 were obtained via the above STAR analysis pipeline.
    STAR
    suggested: (STAR, RRID:SCR_004463)
    For these reads, the fragments from host genome were annotated by corresponding genome annotation reference by bedtools intersectBed6.
    bedtools
    suggested: (BEDTools, RRID:SCR_006646)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.06.06.447293v1 on bioRxiv