SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

  1. Irwin Jungreis
  2. Rachel Sealfon
  3. Manolis Kellis

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Abstract

Despite its overwhelming clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. Here, we use comparative genomics to provide a high-confidence protein-coding gene set, characterize protein-level and nucleotide-level evolutionary constraint, and prioritize functional mutations from the ongoing COVID-19 pandemic. We select 44 complete Sarbecovirus genomes at evolutionary distances ideally-suited for protein-coding and non-coding element identification, create whole-genome alignments, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for all named genes and for 3a, 6, 7a, 7b, 8, 9b, and also ORF3c, a novel alternate-frame gene. By contrast, ORF10, and overlapping-ORFs 9c, 3b, and 3d lack protein-coding signatures or convincing experimental evidence and are not protein-coding. Furthermore, we show no other protein-coding genes remain to be discovered. Cross-strain and within-strain evolutionary pressures largely agree at the gene, amino-acid, and nucleotide levels, with some notable exceptions, including fewer-than-expected mutations in nsp3 and Spike subunit S1, and more-than-expected mutations in Nucleocapsid. The latter also shows a cluster of amino-acid-changing variants in otherwise-conserved residues in a predicted B-cell epitope, which may indicate positive selection for immune avoidance. Several Spike-protein mutations, including D614G, which has been associated with increased transmission, disrupt otherwise-perfectly-conserved amino acids, and could be novel adaptations to human hosts. The resulting high-confidence gene set and evolutionary-history annotations provide valuable resources and insights on COVID-19 biology, mutations, and evolution.

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    SciScore for 10.1101/2020.06.02.130955: (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 UniProt annotations for SARS-CoV-2 were obtained from the UCSC Genome Browser 48 on April 5, 2020.
    UCSC Genome Browser
    suggested: (UCSC Genome Browser, RRID:SCR_005780)
    The Phylogenetic tree was calculated using RAxML 51 using the GTRCATX model.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    FRESCo 29 was run using HYPHY version 2.220180618beta(MP) for Linux on x86_64 on 9-codon windows in each of the NCBI annotated ORFs.
    HYPHY
    suggested: (HyPhy, RRID:SCR_016162)
    However, in Supplementary Table S3, we also classified variants according to our proposed reference gene annotations (fields beginning with New_); when classifying variants in overlapping ORFs 3a/3c and N/9b we classify SNVs relative to the ORF in which the variant is non-synonymous if that is true for only one of the frames, or the ORF for which the amino acid change is more radical (as defined by the blosum62 matrix obtained from biopython version 1.58 53) if it is non-synonymous in both frames, or the larger ORF if the variant is synonymous in both frames.
    biopython
    suggested: (Biopython, RRID:SCR_007173)
    To further test significance of the SNV depletion in S1, we downloaded a larger set of SNVs from the UCSC Table Browser as above on 2020-05-09.
    UCSC Table Browser
    suggested: None

    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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  2. Version published to 10.1101/2020.06.02.130955 on bioRxiv