Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins

  1. Muhammad Hasan
  2. Zhouyi He
  3. Mengqi Jia
  4. Alvin C. F. Leung
  5. Kathiresan Natarajan
  6. Wentao Xu
  7. Shanqi Yap
  8. Feng Zhou
  9. Shihong Chen
  10. Hailei Su
  11. Kaicheng Zhu
  12. Haibin Su

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Abstract

Throughout the coronavirus disease 2019 (COVID-19) pandemic, the continuous genomic evolution of its etiological agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has generated many new variants with enhanced transmissibility and immune escape capabilities. Being an essential mediator of infections and a key target of antibodies, mutations of its spike glycoprotein play a vital role in modulating its evolutionary trajectory. Here, we present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike. Together with analysis of its single amino acid polymorphism (SAP), we propose the use of L -index in quantifying the mutation strength of each amino acid site, such that the evolutionary mutation pattern of the spike glycoprotein can be unravelled.

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  1. Version published to 10.1101/2021.12.29.474427v2 on bioRxiv
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    SciScore for 10.1101/2021.12.29.474427: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The multiple sequence alignment for individual group was conducted consecutively using Clustal Omega.[25].
    Clustal Omega.
    suggested: None

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 17. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

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  3. Version published to 10.1101/2021.12.29.474427v1 on bioRxiv