Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?

  1. Ping Liu
  2. Jing-Zhe Jiang
  3. Xiu-Feng Wan
  4. Yan Hua
  5. Linmiao Li
  6. Jiabin Zhou
  7. Xiaohu Wang
  8. Fanghui Hou
  9. Jing Chen
  10. Jiejian Zou
  11. Jinping Chen

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.02.18.954628: (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
    Genomic assembly and sequence analyses: After examining the high similarity among the samples from three animals, to maximize the coverage of the virus genome, clean reads from three animals were pooled together and de novo assembled using MEGAHIT v1.2.9 [19].
    MEGAHIT
    suggested: (MEGAHIT, RRID:SCR_018551)
    The assembled contigs were used as references for mapping those the rest unmapped reads using Salmon v0.14.1 [20], and multiple rounds were implemented to maximize the mapping (Table S2).
    Salmon
    suggested: (Salmon, RRID:SCR_017036)
    A total of 38 contigs were identified to be highly similar to the 2019-nCoV genome (accession MN908947.3) using BLASTn and tBLASTx.
    BLASTn
    suggested: (BLASTN, RRID:SCR_001598)
    tBLASTx
    suggested: (TBLASTX, RRID:SCR_011823)
    GapFiller v1.10 and SSPACE v3.0 were used to fill gaps and draft pangolin-CoV-2020 genome was constructed with ABACAS v1.3.1 (http://abacas.sourceforge.net/) [21, 22, 23].
    GapFiller
    suggested: None
    SSPACE
    suggested: (SSPACE, RRID:SCR_005056)
    ABACAS
    suggested: (ABACAS, RRID:SCR_015852)
    Multiple sequence alignments were conducted using CLUSTAL Ov1.2.4 [24].
    CLUSTAL
    suggested: (Clustal X , RRID:SCR_017055)
    Simplot analyses were conducted with SimPlot v3.5.1 to determine the sequence similarity among 2019-nCoV (MN908947.3), pangolin-CoV-2020, Bat-CoV-RaTG13 (MN996532.1), and SARS-CoV (AY395003.1) at both the genomic sequence level and at individual gene level [25].
    SimPlot
    suggested: None
    Sequence identity was calculated utilizing p-diatance in MEGA v10.1.7 [26].
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Phylogenetic analyses were performed based on their whole genome sequences, encoding ORFs of RNA-dependent RNA polymerase (RdRp gene), the receptor binding protein spike protein (S gene), small envelope protein (E gene), as well as all other gene sequences were conducted utilizing Mrbayes [27] with 50,000,000 generations and the 25% of the generations as burnin.
    Mrbayes
    suggested: (MrBayes, RRID:SCR_012067)
    Best models were determined by jModeltest v2.1.7 [28].
    jModeltest
    suggested: (jModelTest, RRID:SCR_015244)
    Then, all the trees were visualized and exported as vector diagrams with FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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 10.1371/journal.ppat.1008421
  3. Version published to 10.1101/2020.02.18.954628v1 on bioRxiv