No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

  1. Nathan Smits
  2. Jay Rasmussen
  3. Gabriela O. Bodea
  4. Alberto A. Amarilla
  5. Patricia Gerdes
  6. Francisco J. Sanchez-Luque
  7. Prabha Ajjikuttira
  8. Naphak Modhiran
  9. Benjamin Liang
  10. Jamila Faivre
  11. Ira W. Deveson
  12. Alexander A. Khromykh
  13. Daniel Watterson
  14. Adam D. Ewing
  15. Geoffrey J. Faulkner

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Abstract

No abstract available

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  1. Version published to 10.1016/j.celrep.2021.109530
  2. Version published to 10.1101/2021.05.28.446065v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.05.28.446065: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Further ethics approvals were provided by the Mater Health Services Human Research Ethics Committee (Reference: HREC-15-MHS-52) and the University of Queensland Medical Research Review Committee (Reference:
    Sex as a biological variableHepatocellular carcinoma patient samples: Liver tumour and non-tumour tissue were previously obtained from a HBV-positive patient (HCC32, male, 73yrs) who underwent surgical resection at the Centre Hepatobiliaire, Paul-Brousse Hospital, and made available for research purposes with approval from the French Institute of Medical Research and Health (Reference: 11-047).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: Viral titration was determined by immuno-plaque assay (iPA), as previously described54.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 infection of HEK293T cells: HEK293T cells and African green monkey kidney cells (Vero E6) were maintained in standard Dulbecco’s Modified Eagle Medium (DMEM).
    Vero E6
    suggested: RRID:CVCL_XD71)
    HEK293T viral infection was undertaken as follows: 3×106 HEK293T cells were seeded onto 6-well plates pre-coated with polylysine one day before infection.
    HEK293T
    suggested: None
    Software and Algorithms
    SentencesResources
    350-500ng of each prepared library was sequenced separately on one PromethION (Oxford Nanopore Technologies) flow cell (FLO-PRO002, R9.4.1 chemistry) (Supplementary Table 1).
    PromethION
    suggested: (PromethION, RRID:SCR_017987)
    Sequencing data were deposited in the Sequence Read Archive (SRA) under project PRJEB44816.
    Sequence Read Archive
    suggested: (DDBJ Sequence Read Archive, RRID:SCR_001370)
    ONT bioinformatic analyses: To call non-reference insertions with TLDR23, ONT reads generated here, by Zhang et al.29, and by our previous ONT study of human tissues23 (Supplementary Table 1) were aligned to the human reference genome build hg38 using minimap255 version 2.17 (index parameter: -x map-ont; alignment parameters: -ax map-ont -L -t 32) and samtools56 version 1.12.
    samtools56
    suggested: None
    fa were counted with samtools idxstats.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    PCR primers for the HBV insertion 3’ junction (Fig. 2b and Supplementary Table 2) were designed with Primer3 using the reference genome and closest match HBV sequence (Genbank accession AB602818) as inputs.
    Primer3
    suggested: (Primer3, RRID:SCR_003139)

    Results from OddPub: Thank you for sharing your code and 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.

  4. Version published to 10.1101/2021.05.28.446065v1 on bioRxiv