Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

  1. Jiao-Mei Huang
  2. Syed Sajid Jan
  3. Xiaobin Wei
  4. Yi Wan
  5. Songying Ouyang

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Abstract

The recent global outbreak of viral pneumonia designated as Coronavirus Disease 2019 (COVID-19) by coronavirus (SARS-CoV-2) has threatened global public health and urged to investigate its source. Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13) and clustered together in phylogenetic tree. Furthermore, RaTGl3 also showed 97.43% spike protein similarity with SARS-CoV-2 suggesting that RaTGl3 is the closest strain. However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. In short, our findings propose that homologous recombination has been occurred between bat and pangolin CoVs that triggered cross-species transmission and emergence of SARS-CoV-2, and, during the ongoing outbreak, SARS-CoV-2 is still evolving for its adaptability.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.16.993816: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Host reference genome (pangolin ManJav1.O, GCF_001685135.1) contaminant reads were removed by bowtie2 (v2.3.5.1) [13].
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    Phylogenetic and recombination analysis: The sequences of CoVs were aligned using multiple sequence alignment MAFFT (v7.450) (Katoh et al., 2019).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Aligned sequences were visualized with Jalview (v2.10.3) (Waterhouse et al., 2009).
    Jalview
    suggested: (Jalview, RRID:SCR_006459)
    Poorly aligned regions and gaps were removed by trimAL (v1.4.rev22) (Capellagutiérrez et al., 2009).
    trimAL
    suggested: (trimAl, RRID:SCR_017334)
    Maximum likelihood (ML) phylogenetic trees of whole genome sequences were constructed in IQ-TREE (v1.6.12) (Nguyen et al., 2015).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.03.16.993816v2 on bioRxiv
  3. Version published to 10.1101/2020.03.16.993816v1 on bioRxiv