Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2

  1. Yvonne CF Su
  2. Danielle E Anderson
  3. Barnaby E Young
  4. Feng Zhu
  5. Martin Linster
  6. Shirin Kalimuddin
  7. Jenny GH Low
  8. Zhuang Yan
  9. Jayanthi Jayakumar
  10. Louisa Sun
  11. Gabriel Z Yan
  12. Ian H Mendenhall
  13. Yee-Sin Leo
  14. David Chien Lye
  15. Lin-Fa Wang
  16. Gavin JD Smith

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Abstract

To date, the SARS-CoV-2 genome has been considered genetically more stable than SARS-CoV or MERS-CoV. Here we report a 382-nt deletion covering almost the entire open reading frame 8 (ORF8) of SARS-CoV-2 obtained from eight hospitalized patients in Singapore. The deletion also removes the ORF8 transcription-regulatory sequence (TRS), which in turn enhances the downstream transcription of the N gene. We also found that viruses with the deletion have been circulating for at least four weeks. During the SARS-CoV outbreak in 2003, a number of genetic variants were observed in the human population [1], and similar variation has since been observed across SARS-related CoVs in humans and bats. Overwhelmingly these viruses had mutations or deletions in ORF8, that have been associated with reduced replicative fitness of the virus [2]. This is also consistent with the observation that towards the end of the outbreak sequences obtained from human SARS cases possessed an ORF8 deletion that may be associated with host adaptation [1]. We therefore hypothesise that the major deletion revealed in this study may lead to an attenuated phenotype of SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.11.987222: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: This study was undertaken as part of the national disease outbreak and the response and the protocols were approved by the ethics committee of the National Healthcare Group.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Material from clinical samples was used to inoculate Vero-E6 cells (ATCC®CRL-1586™).
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Ethics statement: This study was undertaken as part of the national disease outbreak and the response and the protocols were approved by the ethics committee of the National Healthcare Group.
    National Healthcare
    suggested: None
    Patient samples were collected under PROTECT (2012/00917), a multi-centred Prospective Study to Detect Novel Pathogens and Characterize Emerging Infections.
    PROTECT
    suggested: (ProTECT, RRID:SCR_004531)
    Raw NGS reads were trimmed by Trimmomatic v0.39 [19] to remove adaptors and low-quality bases.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Genome sequences were assembled and consensus sequences obtained using the BWA algorithm in UGENE v.33.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    UGENE
    suggested: (Unipro UGENE, RRID:SCR_005579)
    The resulting TPM data was generated in Geneious and graphs plotted using ggplot 2 (v3.2.0) in R v3.6.1.
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    Significance between groups was assessed using a one-way analysis of variance (ANOVA) in PRISM v8.3.1.
    PRISM
    suggested: (PRISM, RRID:SCR_005375)
    Genome sequence alignment was performed and preliminary maximum likelihood phylogenies of complete genome were reconstructed using RAxML with 1,000 bootstrap replicates in Geneious R9.0.3 software (Biomatters Ltd).
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    To reconstruct a time-scaled phylogeny, an uncorrelated lognormal relaxed-clock model with an exponential growth coalescent prior and the HKY85+Γ substitution model was used in the program BEAST v1.10.4 [20] to simultaneously estimate phylogeny, divergence times and rates of nucleotide substitution.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The runs were checked for convergence in Tracer v1.7 [21] and that effective sampling size (ESS) values of all parameters was >200.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)

    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

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  2. Version published to 10.1101/2020.03.11.987222v1 on bioRxiv