The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans

  1. Katarzyna Pancer
  2. Aleksandra Milewska
  3. Katarzyna Owczarek
  4. Agnieszka Dabrowska
  5. Michał Kowalski
  6. Paweł P. Łabaj
  7. Wojciech Branicki
  8. Marek Sanak
  9. Krzysztof Pyrc

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Abstract

SARS-CoV-2 genome annotation revealed the presence of 10 open reading frames (ORFs), of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical gene, which was speculated to encode a 38 aa protein. This hypothetical protein does not share sequence similarity with any other known protein and cannot be associated with a function. While the role of this ORF10 was proposed, there is growing evidence showing that the ORF10 is not a coding region. Here, we identified SARS-CoV-2 variants in which the ORF10 gene was prematurely terminated. The disease was not attenuated, and the transmissibility between humans was maintained. Also, in vitro , the strains replicated similarly to the related viruses with the intact ORF10. Altogether, based on clinical observation and laboratory analyses, it appears that the ORF10 protein is not essential in humans. This observation further proves that the ORF10 should not be treated as the protein-coding gene, and the genome annotations should be amended.

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  1. Version published to 10.1371/journal.ppat.1008959
  2. ScreenIT

    SciScore for 10.1101/2020.08.29.257360: (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 variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    All SARS-CoV-2 stocks were generated by infecting monolayers of Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Presence of SARS-CoV-2 material in the collected sample was tested using GeneFinder real-time COVID-19 plus kit (OSANG Healthcare, Korea)
    GeneFinder
    suggested: (GENEFINDER, RRID:SCR_009190)
    OSANG Healthcare
    suggested: None
    NGS sequencing was accomplished using MiSeq v.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Raw sequencing files were demultiplexed using IlluminaBasecallsToFasq procedure from PICARD package and mapped to NC_055512.2 SARS-CoV-2 reference sequence with BwaAndMarkDuplicatesPipelineSpark procedure from GATK v.
    PICARD
    suggested: (Picard, RRID:SCR_006525)
    GATK
    suggested: (GATK, RRID:SCR_001876)

    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:
    • 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.

  3. Version published to 10.1101/2020.08.29.257360v1 on bioRxiv