SARS-CoV-2 Spike Glycoprotein and ACE2 Interaction Reveals Modulation of Viral Entry in Wild and Domestic Animals

  1. Manas Ranjan Praharaj
  2. Priyanka Garg
  3. Veerbhan Kesarwani
  4. Neelam A. Topno
  5. Raja Ishaq Nabi Khan
  6. Shailesh Sharma
  7. Manjit Panigrahi
  8. B. P. Mishra
  9. Bina Mishra
  10. G. Sai Kumar
  11. Ravi Kumar Gandham
  12. Raj Kumar Singh
  13. Subeer Majumdar
  14. Trilochan Mohapatra

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a viral pathogen causing life-threatening diseases in humans. Interaction between the spike protein of SARS-CoV-2 and angiotensin-converting enzyme 2 (ACE2) is a potential factor in the infectivity of a host. In this study, the interaction of SARS-CoV-2 spike protein with its receptor, ACE2, in different hosts was evaluated to predict the probability of viral entry. Phylogeny and alignment comparison of the ACE2 sequences did not lead to any meaningful conclusion on viral entry in different hosts. The binding ability between ACE2 and the spike protein was assessed to delineate several spike binding parameters of ACE2. A significant difference between the known infected and uninfected species was observed for six parameters. However, these parameters did not specifically categorize the Orders into infected or uninfected. Finally, a logistic regression model constructed using spike binding parameters of ACE2, revealed that in the mammalian class, most of the species of Carnivores, Artiodactyls, Perissodactyls, Pholidota, and Primates had a high probability of viral entry. However, among the Proboscidea, African elephants had a low probability of viral entry. Among rodents, hamsters were highly probable for viral entry with rats and mice having a medium to low probability. Rabbits have a high probability of viral entry. In Birds, ducks have a very low probability, while chickens seemed to have medium probability and turkey showed the highest probability of viral entry. The findings prompt us to closely follow certain species of animals for determining pathogenic insult by SARS-CoV-2 and for determining their ability to act as a carrier and/or disseminator.

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  1. Version published to 10.3389/fmed.2021.775572
  2. Version published to 10.1101/2020.05.08.084327v4 on bioRxiv
  3. Version published to 10.1101/2020.05.08.084327v3 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.05.08.084327: (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
    Phylogenetic analysis: Phylogenetic analysis of the protein sequences was done using MEGA 6.0[38].
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The aligned sequences were then analyzed for the best nucleotide substitution model on the basis of Bayesian information criterion scores using the JModelTest software v2.1.7[40].
    JModelTest
    suggested: (jModelTest, RRID:SCR_015244)
    Homology modeling: The Structures of novel coronavirus spike receptor-binding domain complexed with its receptor - ACE2, that were determined through X-ray diffraction are available at PDB database with IDs 6LZG [25], 6M0J [41] and 6VW1 [42]These available ACE2 models from PDB database were used for homology modeling using SWISS-MODEL[43], which was accessed through ExPASy web server.
    ExPASy
    suggested: None
    Five docked complexes were generated from GRAMM-X for each X-ray crystallography model in each species and post-docking analyses was carried out using Chimera software[46] and PRODIGY [47].
    Chimera
    suggested: (Chimera, RRID:SCR_002959)
    Further, in addition to delta G and RMSD, in FoldX software [48] several parameters were estimated for all these selected docked structures (for 432 models (48 hosts × 3 X-ray Crystallography models × 3 selected docking complexes) were analyzed), These parameters include - IntraclashesGroup1, IntraclashesGroup2
    FoldX
    suggested: (FoldX, RRID:SCR_008522)

    Results from OddPub: Thank you for sharing your 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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  5. Version published to 10.1101/2020.05.08.084327v2 on bioRxiv
  6. Version published to 10.1101/2020.05.08.084327v1 on bioRxiv