A tale of three SARS-CoV-2 variants with independently acquired P681H mutations in New York State

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

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Abstract

Several SARS-CoV-2 variants of concern have independently acquired some of the same Spike protein mutations - notably E484K, N501Y, S477N, and K417T - associated with increased viral transmission and/or reduced sensitivity to neutralization by antibodies. Repeated evolution of the same mutations, particularly in variants that are now rapidly spreading in various regions of the world, suggests a fitness advantage. Mutations at position P681 in Spike – possibly affecting viral transmission - have also evolved multiple times, including in two variants of concern. Here, we describe three variants circulating in New York State that have independently acquired a P681H mutation and the different trajectories they have taken. While one variant rose to high prevalence since later summer 2020 it appears to be in decline. The other two variants were more recently detected in New York and harbor additional Spike mutations that might be cause for continued monitoring. The latter two P681H variants have shown moderate increases in prevalence but ultimately all might be subject to the same fate as more competitive variants come to dominate the scene.

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    SciScore for 10.1101/2021.03.10.21253285: (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
    Stacked area plots and bubble maps were rendered in R v4.0.3 (https://www.r-project.org/) with ggplot2 and map packages and coloring provided by the viridis package.
    https://www.r-project.org/
    suggested: (R Project for Statistical Computing, RRID:SCR_001905)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    In summary, a total of 2689 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: 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

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  2. Version published to 10.1101/2021.03.10.21253285v1 on medRxiv