A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

  1. Simon Pollett
  2. Matthew A. Conte
  3. Mark Sanborn
  4. Richard G. Jarman
  5. Grace M. Lidl
  6. Kayvon Modjarrad
  7. Irina Maljkovic Berry

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Abstract

The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.

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  1. Version published to 10.1038/s41598-021-96626-8
  2. ScreenIT

    SciScore for 10.1101/2021.03.07.434287: (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
    Datasets were aligned using MAFFT (33), with manual alignment thereafter in MEGA v6.0 (
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The remaining 100,296 genomes were aligned to the MN908947.3 reference using mafftc (7.471) in the MAFFT software (33)
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A maximum likelihood phylogeny was inferred using the PhyML software (49), with aLRT for node support and tips labeled by date of collection.
    PhyML
    suggested: (PhyML, RRID:SCR_014629)
    Time-scaled genealogies of these viruses were inferred using the BEAST software 1.8.4 (52).
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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.

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  3. Version published to 10.1101/2021.03.07.434287v1 on bioRxiv