Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic

  1. Lauro Velazquez-Salinas
  2. Selene Zarate
  3. Samantha Eberl
  4. Douglas P. Gladue
  5. Isabel Novella
  6. Manuel V. Borca

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Abstract

In this study, we analyzed full-length SARS-CoV-2 genomes from multiple countries to determine early trends in the evolutionary dynamics of the novel COVID-19 pandemic. Results indicated SARS-CoV-2 evolved early into at least three phylogenetic groups, characterized by positive selection at specific residues of the accessory proteins ORF3a and ORF8. Also, we are reporting potential relevant sites under positive selection at specific sites of non-structural proteins nsp6 and helicase. Our analysis of co-evolution showed evidence of epistatic interactions among sites in the genome that may be important in the generation of variants adapted to humans. These observations might impact not only public health but also suggest that more studies are needed to understand the genetic mechanisms that may affect the development of therapeutic and preventive tools, like antivirals and vaccines. Collectively, our results highlight the identification of ongoing selection even in a scenario of conserved sequences collected over the first 3 months of this pandemic.

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  1. Version published to 10.3389/fmicb.2020.550674
  2. ScreenIT

    SciScore for 10.1101/2020.04.10.035964: (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 resulting file was analyzed with Tracer 1.6 to check for convergence and to determine the Burnin proportion (Rambaut et al., 2018).
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    Finally, TreeAnnotator was used to build the maximum clade credibility tree, which was visualized with FigTree 1.4.3 (http://tree.bio.ed.ac.uk/software/figtree).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    This analysis was conducted using MEGA 7 (Kumar et al., 2016).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Evidence of directional selection was assessed on amino acid sequences using the Directional Evolution of Protein Sequences (DEPS) method, implemented on the Datamonkey webserver (classic) (Delport et al., 2010).
    Datamonkey
    suggested: (DataMonkey, RRID:SCR_010278)

    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.

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  3. Version published to 10.1101/2020.04.10.035964v1 on bioRxiv