Assessing SARS-CoV-2 spatial phylogenetic structure: Evidence from RNA and protein sequences

  1. Leandro R. Jones
  2. Julieta M. Manrique

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We show that the virus is a complex of slightly different variants that are unevenly distributed on Earth, and demonstrate that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were associated with ancestral amino acidic mutations. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersal. Based on previous studies, the possibility that this could significantly affect the virus phenotype is not remote.

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  1. Version published to 10.1101/2020.06.05.135954v2 on bioRxiv
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    SciScore for 10.1101/2020.06.05.135954: (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
    The selected data (genomes with no non-DNA characters) were aligned with Mafft (Katoh and Toh, 2008) (details below) and the obtained alignment was visually inspected with Jalview (Waterhouse et al., 2009).
    Mafft
    suggested: (MAFFT, RRID:SCR_011811)
    Jalview
    suggested: (Jalview, RRID:SCR_006459)
    The small dataset was phylogenetically analyzed with PhyML version 3.3 (Guindon et al., 2010) under a generalized time-reversible model with a proportion of invariable sites and 4 rate categories.
    PhyML
    suggested: (PhyML, RRID:SCR_014629)

    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

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  3. Version published to 10.1101/2020.06.05.135954v1 on bioRxiv