A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species

  1. Torstein Tengs
  2. Charles F. Delwiche
  3. Christine Monceyron Jonassen

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Abstract

Unprecedented quantities of sequence data have been generated from the newly emergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of COVID-19. We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.29.177030: (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.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    To characterize the specific genotype of s2m found in SARS-CoV-2, BLASTN (Altschul, et al. 1990) was used to search the entire virus section of GenBank using all s2m sequence genotypes reported in the literature (n = 97) (Jonassen, et al. 1998; Robertson, et al. 2005; Tengs, et al. 2013; Tengs and Jonassen 2016) as query sequences.
    BLASTN
    suggested: (BLASTN, RRID:SCR_001598)
    For the phylogenetic analyses, sequences were aligned using the Clustal W algorithm (Thompson, et al. 1994) and maximum likelihood analysis were performed using MEGA X (Kumar, et al. 2018).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.

  2. Version published to 10.1101/2020.06.29.177030 on bioRxiv