The localized rise of a B.1.526 SARS-CoV-2 variant containing an E484K mutation in New York State

  1. Erica Lasek-Nesselquist
  2. Pascal Lapierre
  3. Erasmus Schneider
  4. Kirsten St. George
  5. Janice Pata

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Abstract

The E484K mutation in the spike protein of SARS CoV-2 contributes to immune escape from monoclonal antibodies as well as neutralizing antibodies in COVID-19 convalescent plasma. It appears in two variants of concern – B.1.351 and P.1 - but has evolved multiple times in different SARS-CoV-2 lineages, suggesting an adaptive advantage. Here we report on the emergence of a 484K variant in the B.1.526 lineage that has recently become prevalent in New York State, particularly in the New York City metropolitan area. In addition to the E484K mutation, these variants also harbor a D235G substitution in spike that might help to reduce the efficacy of neutralizing antibodies.

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    SciScore for 10.1101/2021.02.26.21251868: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: IRB Approval: This work was approved by the New York State Department of Health Institutional Review Board, under study numbers 02-054 and 07-022.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, reads were trimmed with TrimGalore (https://github.com/FelixKrueger/TrimGalore) and aligned to the reference assembly MN908947.3 (strain Wuhan-Hu-1) by BWA (Li & Durbin 2009).
    TrimGalore
    suggested: None
    BWA
    suggested: (BWA, RRID:SCR_010910)
    In summary, a total of 2155 genomes >27 Kb in length were aligned in MAFFT v7.475 (Katoh & Standley 2013), a maximum likelihood phylogeny was generated with IQ-TREE v2.0.3 (Nguyen et al. 2015) under a GTR+G4 nucleotide substitution model, and divergence times as well as ancestral traits were inferred with TreeTime (Sagulenko et al. 2018).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    There are also caveats to consider. The increase in frequency of 484K and 477N variants might be due to stochastic processes unrelated to phenotype. While we would expect an initial localized spike in the number of variants that confer a selective advantage, we have not observed a substantial spread of either B.1.526 484K or 477N from the NYC metropolitan area to other regions of the state since their first detection. However, the combination of two mutations that potentially provide immune escape in a SARS-CoV-2 lineage that has rapidly risen in frequency warrants further monitoring.

    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

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  2. Version published to 10.1101/2021.02.26.21251868v1 on medRxiv