Pangolin homology associated with 2019-nCoV

  1. Tao Zhang
  2. Qunfu Wu
  3. Zhigang Zhang

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Abstract

To explore potential intermediate host of a novel coronavirus is vital to rapidly control continuous COVID-19 spread. We found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019-nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has similar pathogenic potential to 2019-nCoV, and would be helpful to trace the origin and probable intermediate host of 2019-nCoV.

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    SciScore for 10.1101/2020.02.19.950253: (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
    Raw reads were first adaptor- and quality-trimmed using the Trimmomatic program (version 0.39)(10).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    For removing host contamination, Bowtie2 (version 2.3.4.3) (11)was used to map clean reads to the host reference genome of Manis javanica (NCBI Project ID: PRJNA256023)
    Bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    Mapping coverage and depth were produced using Samtools (version 1.9)(13).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Contigs were taxonomically annotated using BLAST 2.9.0+ against 2845 Coronavirus reference genomes (Table S1).
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Other coronavirus genomes were downloaded ViPR database (https://www.viprbrc.org/brc/home.spg?decorator=corona) on 6 February 2020.
    ViPR
    suggested: (vipR, RRID:SCR_010685)
    Aligned contigs were merged into consensus scaffold with BioEdit version 7.2.5 (http://www.mybiosoftware.com/bioedit-7-0-9-biological-sequence-alignment-editor.html) following manually quality checking.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    Phylogenetic relationship analysis: Sequence alignment was carried out using MUSCLE software(14).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)

    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.

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  2. Version published to 10.1101/2020.02.19.950253v1 on bioRxiv