Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

  1. Tommy Tsan-Yuk Lam
  2. Marcus Ho-Hin Shum
  3. Hua-Chen Zhu
  4. Yi-Gang Tong
  5. Xue-Bing Ni
  6. Yun-Shi Liao
  7. Wei Wei
  8. William Yiu-Man Cheung
  9. Wen-Juan Li
  10. Lian-Feng Li
  11. Gabriel M Leung
  12. Edward C. Holmes
  13. Yan-Ling Hu
  14. Yi Guan

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, provisionally termed 2019-nCoV. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, the identity of any intermediate host facilitating transfer to humans is unknown. Here, we report the identification of 2019-nCoV related coronaviruses in pangolins ( Manis javanica ) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin associated CoVs that belong to two sub-lineages of 2019-nCoV related coronaviruses, including one very closely related to 2019-nCoV in the receptor-binding domain. The discovery of multiple lineages of pangolin coronavirus and their similarity to 2019-nCoV suggests that pangolins should be considered as possible intermediate hosts for this novel human virus and should be removed from wet markets to prevent zoonotic transmission.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.02.13.945485: (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

    Experimental Models: Cell Lines
    SentencesResources
    Using the intestine-lung mixed sample we were able to isolate a novel Betacoronavirus using the Vero-E6 cell line (Extended Data Figure S1).
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Both BLASTn and BLASTx were used to search against a local virus database, utilizing the data available at NCBI/GenBank.
    BLASTn
    suggested: (BLASTN, RRID:SCR_001598)
    BLASTx
    suggested: (BLASTX, RRID:SCR_001653)
    These reads were quality assessed, cleaned and assembled into contigs by both de novo (MEGAHIT v1.1.312) and using reference (BWA v0.7.1313) assembly methods, with BetaCoV/Wuhan/WIV04/2019 as reference.
    MEGAHIT
    suggested: (MEGAHIT, RRID:SCR_018551)
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Liu et al. recently published a meta-transcriptomic study of pangolins7 and deposited 21 RNA-seq raw files on the SRA database (https://www.ncbi.nlm.nih.gov/sra).
    https://www.ncbi.nlm.nih.gov/sra
    suggested: (NCBI Sequence Read Archive (SRA, RRID:SCR_004891)
    We screened these raw read files using BLAST methods and found that five (SRR10168374, SRR10168376, SRR10168377, SRR10168378 and SRR10168392) contained reads that mapped to 2019-nCoV.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    These reads were subjected to quality assessment, cleaning and then de novo assembly using MEGAHIT12 and reference assembly using BWA13.
    BWA13
    suggested: None
    We constructed a multiple sequence alignment of their complete genomes and individual genes using MAFFT v7.27314.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum likelihood phylogenies were estimated using PhyML v3.115, utilizing the GTR+I+Γ model of nucleotide substitution with 1,000 bootstrap replicates.
    PhyML
    suggested: (PhyML, RRID:SCR_014629)

    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 10.1101/2020.02.13.945485 on bioRxiv