No detectable signal for ongoing genetic recombination in SARS-CoV-2

  1. Damien Richard
  2. Christopher J. Owen
  3. Lucy van Dorp
  4. François Balloux

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Abstract

The COVID-19 pandemic has led to an unprecedented global sequencing effort of its viral agent SARS-CoV-2. The first whole genome assembly of SARS-CoV-2 was published on January 5 2020. Since then, over 150,000 high-quality SARS-CoV-2 genomes have been made available. This large genomic resource has allowed tracing of the emergence and spread of mutations and phylogenetic reconstruction of SARS-CoV-2 lineages in near real time. Though, whether SARS-CoV-2 undergoes genetic recombination has been largely overlooked to date. Recombination-mediated rearrangement of variants that arose independently can be of major evolutionary importance. Moreover, the absence of recombination is a key assumption behind the application of phylogenetic inference methods. Here, we analyse the extant genomic diversity of SARS-CoV-2 and show that, to date, there is no detectable hallmark of recombination. We assess our detection power using simulations and validate our method on the related MERS-CoV for which we report evidence for widespread genetic recombination.

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    SciScore for 10.1101/2020.12.15.422866: (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
    SARS-CoV-2 dataset: All 6,546 SARS-CoV-2 high quality genomes (containing less than 5% of “N” and being >29,000 bp long) sampled during the month of September 2020 available on GISAID (as of October 15th 2020) were downloaded and profile aligned to the Wuhan-Hu-1 reference genome (GenBank accession MN908947; GISAID ID EPI_ISL_402125) using MAFFT v7.471 [51].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Following construction of a maximum likelihood tree using IQTree Covid-release [52], 29.6% of SNPs were identified as homoplasic by HomoplasyFinder [53].
    HomoplasyFinder
    suggested: (HomoplasyFinder, RRID:SCR_017300)

    Results from OddPub: Thank you for sharing your code and data.

    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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  2. Version published to 10.1101/2020.12.15.422866v1 on bioRxiv