Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants

  1. Veronika Tchesnokova
  2. Hemantha Kulasekara
  3. Lydia Larson
  4. Victoria Bowers
  5. Elena Rechkina
  6. Dagmara Kisiela
  7. Yulia Sledneva
  8. Debarati Choudhury
  9. Iryna Maslova
  10. Kai Deng
  11. Kirthi Kutumbaka
  12. Hao Geng
  13. Curtis Fowler
  14. Dina Greene
  15. James Ralston
  16. Mansour Samadpour
  17. Evgeni Sokurenko

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Abstract

We report that there is a recent global expansion of numerous independent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutation L452R in the receptor-binding domain (RBD) of the spike protein. The massive emergence of L452R variants was first linked to lineage B.1.427/B.1.429 (clade 21C) that has been spreading in California since November and December 2020, originally named CAL.20C and currently variant of interest epsilon.

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  1. Version published to 10.1128/jcm.00921-21
  2. Version published to 10.1101/2021.02.22.432189v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.02.22.432189: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The Western Institutional Review Board (Puyallup, WA) provided institutional biosafety committee services to Institute for Environmental Health by approving consent forms and human research safety protocols.
    Consent: The Western Institutional Review Board (Puyallup, WA) provided institutional biosafety committee services to Institute for Environmental Health by approving consent forms and human research safety protocols.
    Randomization20A) and 50 randomly chosen B.1.429 (CAL.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequences were analyzed using BioEdit 7.2 and MEGA 7 Software.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    Whole genome sequencing: WGS was performed by IEH on MiSeq Illumina instrument; each sample was subjected to two individual rounds of sequencing.
    WGS
    suggested: None
    20C) as well as the closely related L452 ancestors from both lineages were aligned and used to build total and synonymous-only phylogenetic trees using MEGA 7 software.
    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.

  4. Version published to 10.1101/2021.02.22.432189v1 on bioRxiv