Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

  1. Joana Damas
  2. Graham M. Hughes
  3. Kathleen C. Keough
  4. Corrie A. Painter
  5. Nicole S. Persky
  6. Marco Corbo
  7. Michael Hiller
  8. Klaus-Peter Koepfli
  9. Andreas R. Pfenning
  10. Huabin Zhao
  11. Diane P. Genereux
  12. Ross Swofford
  13. Katherine S. Pollard
  14. Oliver A. Ryder
  15. Martin T. Nweeia
  16. Kerstin Lindblad-Toh
  17. Emma C. Teeling
  18. Elinor K. Karlsson
  19. Harris A. Lewin

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Abstract

The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low . Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.

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    SciScore for 10.1101/2020.04.16.045302: (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
    The protein sequences were predicted using AUGUSTUS v3.3.2 (71) or CESAR v2.0 (72) and the translated protein sequences were checked against the human ACE2 orthologue.
    AUGUSTUS
    suggested: (Augustus, RRID:SCR_008417)
    CESAR
    suggested: (UVa W.M. Keck Biomedical Mass Spectrometry Laboratory, RRID:SCR_012589)
    The source, and accession numbers for the genomes or proteins retrieved from NCBI are listed in Dataset S1.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    To assure alignment robustness, the full set of coding and protein sequences were aligned independently using Clustal Omega (73), MUSCLE (74) and COBALT (75) all with default parameters.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    Additional structural visualizations were generated in Pymol (78).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    Human variants analysis: All variants at the 25 residues critical for effective SARS-CoV-2-ACE2 binding (11, 21, 79) were compiled from from dbSNP (31), 1KGP (32), Topmed (33), UK10K (34) and CHINAMAP (28).
    dbSNP
    suggested: (dbSNP, RRID:SCR_002338)
    Identifying sites undergoing positive selection: Signatures of site-specific positive selection in the ACE2 receptor were explored using CODEML, part of the Phylogenetic Analysis using Maximum Likelihood (PAML, (83)) suite of software.
    PAML
    suggested: (PAML, RRID:SCR_014932)
    A codon alignment of the 64 mammals was generated using pal2nal (84) with protein alignments generated with Clustal Omega (73) and their respective CDS sequences.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    PhyloFit and phyloP are both part of the PHAST package v1.4 (85, 86).
    PHAST
    suggested: (PHAST, RRID:SCR_003204)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    These results are inconsistent with transfection studies using civet ACE2 receptors expressed in HeLa cells (1), although these experiments have limitations as discussed above. While carnivores closely related to dogs (dingos, wolves and foxes) all scored low, experimental data supporting infection in dogs were inconsistent (47, 50, 59) so no conclusions can be drawn. Pangolins: Considerable controversy surrounds reports that pangolins can serve as an intermediate host for SARS-CoV-2. Pangolins were proposed as a possible intermediate host (22) and have been shown to harbor related coronaviruses. In our study, ACE2 of Chinese pangolin (Manis pentadactyla), Sunda pangolin (Manis javanica), and white bellied pangolin (Phataginus tricuspis) had low or very low binding score for SARS-CoV-2 S. Neither experimental infection nor in vitro infection with SARS-CoV-2 has been reported for pangolins. As for ferrets and bats, if SARS-CoV-2 infects pangolins it may be using a receptor other than ACE2, based on our analysis. Other vertebrates: Our analysis of 29 orders of fishes, 29 orders of birds, 3 orders of reptiles and 2 orders of amphibians predicts that the ACE2 proteins of species within these vertebrate classes are not likely to bind SARS-CoV-2 S. Thus, vertebrate classes other than mammals are not likely to be an intermediate host or reservoir for the virus, despite predictions reported in a recent study (45), unless SARS-CoV-2 can use another receptor for infection. With many di...

    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.

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  2. Version published to 10.1101/2020.04.16.045302 on bioRxiv