Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States

  1. Adrian A. Pater
  2. Michael S. Bosmeny
  3. Christopher L. Barkau
  4. Katy N. Ovington
  5. Ramadevi Chilamkurthy
  6. Mansi Parasrampuria
  7. Seth B. Eddington
  8. Abadat O. Yinusa
  9. Adam A. White
  10. Paige E. Metz
  11. Rourke J. Sylvain
  12. Madison M. Hebert
  13. Scott W. Benzinger
  14. Koushik Sinha
  15. Keith T. Gagnon

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Abstract

Genomic surveillance can lead to early identification of novel viral variants and inform pandemic response. Using this approach, we identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.). The earliest sequenced genomes of this variant, referred to as 20C-US, can be traced to Texas in late May of 2020. This variant circulated in the U.S. uncharacterized for months and rose to recent prevalence during the third pandemic wave. It initially acquired five novel, relatively unique non-synonymous mutations. 20C-US is continuing to acquire multiple new mutations, including three independently occurring spike protein mutations. Monitoring the ongoing evolution of 20C-US, as well as other novel emerging variants, will be essential for understanding SARS-CoV-2 host adaptation and predicting pandemic outcomes.

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  1. Version published to 10.1101/2021.01.11.426287v2 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.01.11.426287: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    RandomizationFrom each of these subsets, Nextstrain attempts to randomly pick an equal number of samples.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequencing was performed with Oxford Nanopore Technology’s MinION platform using ARTIC Network protocol (https://artic.network/ncov-2019) with slight modifications to the protocol.
    Oxford Nanopore
    suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
    MinION
    suggested: (MinION, RRID:SCR_017985)
    Briefly, the Augur pipeline utilized by Nextstrain filters sequences for metadata values and N content before aligning them using MAFFT (30).
    Augur
    suggested: None
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The pipeline conducts a maximum likelihood phylogenetic analysis using the general time reversible model allowing for invariant sites and a gamma distribution (GTR+I+G) in IQ-TREE (31).
    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

    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.

  3. Version published to 10.1101/2021.01.11.426287v1 on bioRxiv