Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

  1. Han Mei
  2. Sergei Kosakovsky Pond
  3. Anton Nekrutenko

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Abstract

The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE—the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements—places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.

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  1. Version published to 10.1093/molbev/msab265
  2. ScreenIT

    SciScore for 10.1101/2021.06.14.448413: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Coronavirus entries retrieval and filter: The 35,152 coronaviral entries in the NCBI taxonomy database were sorted by length, and only those larger than 14,945 nt were kept, leaving a total of 4,939 genomes.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    Amino acid alignment and nucleotide alignment of the overlap region: For all δ-coronavirus entries in Table S1, the first 13 amino acids of ORF1b were taken to generate a consensus sequence using WebLogo (Crooks et al. 2004).
    WebLogo
    suggested: (WEBLOGO, RRID:SCR_010236)
    We mapped individual sequences to the NCBI reference genome (NC_045512) using a codon-aware extension to the Smith-Waterman algorithm implemented in HyPhy (Pond et al. 2005; Gianella et al. 2011) translated mapped sequence to amino-acids, and performed multiple protein sequence alignment with the auto settings function of MAFFT (version 7.453) (Katoh and Standley 2013).
    HyPhy
    suggested: (HyPhy, RRID:SCR_016162)
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.06.14.448413v1 on bioRxiv