Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection

  1. Vaibhav Upadhyay
  2. Casey Patrick
  3. Alexandra Lucas
  4. Krishna M. G. Mallela

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  1. Version published to 10.1021/acs.biochem.2c00132
  2. Version published to 10.1101/2021.12.23.474050v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.12.23.474050: (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.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cloning and expression of WT RBD and its mutants, ACE2 and antibodies in ScFv format: The genes encoding WT RBD, ACE2 and the antibodies (CC12.1, LY-CoV555 and REGN10987) in ScFv format were commercially obtained from Twist Biosciences carrying BamH1 and Xho1 restriction sites on the 5’ and 3’ end respectively.
    ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    The genes ware introduced into the modified pcDNA3.4 TOPO mammalian expression vector using BamH1 and Xho1 site.
    pcDNA3.4
    suggested: RRID:Addgene_131198)
    Software and Algorithms
    SentencesResources
    The protein expression levels were compared using SDS-PAGE followed by quantitative densitometric analysis of Coomassie stained protein bands using Image-J software.
    Image-J
    suggested: (ImageJ, RRID:SCR_003070)

    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.
    • No funding statement was detected.
    • 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 10.1101/2021.12.23.474050v1 on bioRxiv