Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

  1. Ahmed M. Moustafa
  2. Colleen Bianco
  3. Lidiya Denu
  4. Azad Ahmed
  5. Brandy Neide
  6. John Everett
  7. Shantan Reddy
  8. Emilie Rabut
  9. Jasmine Deseignora
  10. Michael D. Feldman
  11. Kyle G. Rodino
  12. Frederic Bushman
  13. Rebecca M. Harris
  14. Josh Chang Mell
  15. Paul J. Planet

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Abstract

Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote “escape” from neutralizing antibodies in vitro . We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

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  1. ScreenIT

    SciScore for 10.1101/2021.04.21.440801: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: The sample was obtained by as part of routine clinical care, solely for non-research purposes, carrying minimal risk, and were therefore granted a waiver of informed consent as reviewed under protocol number under IRB 21-018478.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, WGS of extracted viral RNA was performed as previously described using Paragon Genomics CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel17,18.
    WGS
    suggested: None
    All the high coverage SARS-CoV-2 genomes (n=236) were assigned a clonal complex using the GNUVID v2.2 database (version January 6th 2021)15.
    GNUVID
    suggested: None
    Temporal plots were plotted in GraphPad Prism v7.0a.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.
    • No funding statement was detected.
    • 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.

  2. Version published to 10.1101/2021.04.21.440801 on bioRxiv