Uneven growth of SARS-CoV-2 clones evidenced by more than 500,000 whole-genome sequences

  1. Hong-Li Zeng
  2. Yue Liu
  3. Kaisa Thorell
  4. Rickard Nordén
  5. Erik Aurell

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Abstract

We have computed the frequencies of the alleles of the “UK variant” (B.1.1.7) and “South Africa variant” (B.1.351) of SARS-CoV-2 from the large GISAID repository. We find that the frequencies of the mutations in UK variant overall rose towards the end of 2020, as widely reported in the literature and in the general press. However, we also find that these frequencies vary in different patterns rather than in concert. For South Africa variant we find a more complex scenario with frequencies of some mutations rising and some remaining close to zero. Our results point to that what is generally reported as one variant is in fact a collection of variants with different genetic characteristics.

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    SciScore for 10.1101/2021.04.06.437914: (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
    Multiple-Sequence Alignment (MSA): Multiple sequence alignments (MSAs) were constructed with the online alignment server MAFFT (10, 11) with the reference sequence “Wuhan-Hu-1” with the Genbank accession number “MN908947.3”.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Frequency computations and visualizations: The allele frequencies and the visualizations were both done using MATLAB R2020a on “hlz”.
    MATLAB
    suggested: (MATLAB, RRID:SCR_001622)

    Results from OddPub: Thank you for sharing your code.

    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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  2. Version published to 10.1101/2021.04.06.437914v1 on bioRxiv