Which animals are at risk? Predicting species susceptibility to Covid-19

  1. MR Alexander
  2. CT Schoeder
  3. JA Brown
  4. CD Smart
  5. C Moth
  6. JP Wikswo
  7. JA Capra
  8. J Meiler
  9. W Chen
  10. MS Madhur

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Abstract

In only a few months, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, leaving physicians, scientists, and public health officials racing to understand, treat, and contain this zoonotic disease. SARS-CoV-2 has made the leap from animals to humans, but little is known about variations in species susceptibility that could identify potential reservoir species, animal models, and the risk to pets, wildlife, and livestock. While there is evidence that certain species, such as cats, are susceptible, the vast majority of animal species, including those in close contact with humans, have unknown susceptibility. Hence, methods to predict their infection risk are urgently needed. SARS-CoV-2 spike protein binding to angiotensin converting enzyme 2 (ACE2) is critical for viral cell entry and infection. Here we identified key ACE2 residues that distinguish susceptible from resistant species using in-depth sequence and structural analyses of ACE2 and its binding to SARS-CoV-2. Our findings have important implications for identification of ACE2 and SARS-CoV-2 residues for therapeutic targeting and identification of animal species with increased susceptibility for infection on which to focus research and protection measures for environmental and public health.

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  1. ScreenIT

    SciScore for 10.1101/2020.07.09.194563: (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
    In the absence of a published sequence and accession number, ACE2 protein sequence for the lion (Panthera leo) was assembled using TBLASTN (National Center for Biotechnology Information) with tiger ACE2 protein sequence as the query (Extended Data Table
    TBLASTN
    suggested: (TBLASTN, RRID:SCR_011822)
    Protein sequences were loaded into EMBL-EBI web interface implementation of MAFFT for multiple sequence alignment using default settings (https://www.ebi.ac.uk/Tools/msa/mafft/).20 Resulting alignment was uploaded to ESPript 3.0 to generate a graphical version of the alignment (http://espript.ibcp.fr/ESPript/ESPript/), including annotation of secondary structure based on Protein Data Bank (PDB) structure 1r42 of human ACE2.42 A treedyn format tree diagram representing similarity of ACE2 protein sequence across species was generated using phylogeny.fr (https://www.phylogeny.fr/).43,44
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    http://espript.ibcp.fr/ESPript/ESPript/
    suggested: (ESPript 2.2, RRID:SCR_006587)
    NCBI Taxonomy Browser was used to generate a taxonomic tree of phylogenetic relationships amongst species as a Phylogeny Inference Package (PHYLIP) tree.45 Final visualization was performed using the interactive Tree of Life (iTOL) tree viewer v 5.5.1 (https://itol.embl.de/).46
    NCBI Taxonomy Browser
    suggested: None
    PHYLIP
    suggested: (PHYLIP, RRID:SCR_006244)
    Evaluation was performed using the numpy, pandas, matplotlib and seaborn libraries in Python 3.7, PyMOL 2.752-54 and GraphPad Prism version 8.3.0 for Windows (GraphPad Software, San Diego, California).
    matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)
    Python
    suggested: (IPython, RRID:SCR_001658)
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Prediction of glycosylation sites: The NetNGlyc 1.0 server (http://www.cbs.dtu.dk/services/NetNGlyc/) was used to predict glycosylation sites.
    NetNGlyc
    suggested: (NetNGlyc, RRID:SCR_001570)
    An R implementation of this susceptibility score algorithm was also developed in RStudio.
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    Statistical analysis: Contingency testing was performed with Fisher’s exact test as a two-sided comparison and alpha equal to 0.05 using GraphPad Prism version 8.2.1 (GraphPad Software, Inc.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

    About SciScore

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  2. Version published to 10.1101/2020.07.09.194563v1 on bioRxiv