Emergence of the E484K Mutation in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage B.1.1.345 in Upstate New York

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Abstract

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.345 variant carrying the E484K mutation was detected in 4 patients with no apparent epidemiological association from a hospital network in upstate New York. Subsequent analysis identified an additional 11 B.1.1.345 variants from this region between December 2020 and February 2021.

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  1. Our take

    This study, available as a preprint and thus not yet peer-reviewed, described the identification of a new SARS-Cov-2 variant (B.1.220 with the E484K mutation) in Upstate New York in early 2021. The E484K mutation has been identified in other variants of concern, including 501Y.V2/B.1.351 identified first in South Africa, and P.1. identified first in Brazil. Some studies suggest that this mutation may lead to reduced vaccine efficacy as well as antibody-based treatment and prevention of COVID-19; recent clinical data indicate that the Pfizer, Moderna, and J&J vaccines are still protective against other variants with the E484K mutation. The independent emergence of E484K in different SARS-CoV-2 variant backgrounds is concerning, as it implies that this mutation provides a fitness advantage to the virus, even in the …

  2. SciScore for 10.1101/2021.03.11.21253231: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Bioinformatic Analysis of SARS-CoV-2 genomes: Miseq read data was trimmed for adapters and low quality sequence using BBduk v38.79 (https://sourceforge.net/projects/bbmap/).
    Miseq
    suggested: (A5-miseq, RRID:SCR_012148)
    Nucleotide alignments were performed with Muscle23 followed by trimming of ambiguous/under-represented sequence at the 5’/3’ ends of the alignment in Geneious.
    Geneious
    suggested: (Geneious, RRID:SCR_010519)

    Results from OddPub: Thank you for sharing your code.


    Results …