An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

  1. Sudhir Kumar
  2. Qiqing Tao
  3. Steven Weaver
  4. Maxwell Sanderford
  5. Marcos A Caraballo-Ortiz
  6. Sudip Sharma
  7. Sergei L K Pond
  8. Sayaka Miura

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Abstract

Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).

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  1. Version published to 10.1093/molbev/msab118
  2. Version published to 10.1101/2020.09.24.311845v3 on bioRxiv
  3. Version published to 10.1101/2020.09.24.311845v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.09.24.311845: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    We mapped individual sequences to the NCBI reference genome (NC_045512) using a codon-aware extension to the Smith-Waterman algorithm implemented in HyPhy34 (https://github.com/veg/hyphy-analyses/tree/master/codon-msa), translated mapped sequence to amino-acids, and performed multiple protein sequence alignment with the auto settings function of MAFFT (version 7.453)35.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The alignment was visually inspected and adjusted in Geneious Prime 2020.2.2 (https://www.geneious.com).
    https://www.geneious.com
    suggested: (Geneious, RRID:SCR_010519)
    We noted that the earliest sample included in GISAID (ID: EPI_ISL_402123) was collected on December 24, 2019, although the NCBI website lists its collection date as December 23, 2019 (GenBank ID: MT019529).
    NCBI
    suggested: (NCBI, RRID:SCR_006472)

    Results from OddPub: Thank you for sharing your data.

    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.

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  5. Version published to 10.1101/2020.09.24.311845v1 on bioRxiv