SARS-CoV-2 Spike Glycoprotein Receptor Binding Domain is Subject to Negative Selection with Predicted Positive Selection Mutations

  1. You Li
  2. Ye Wang
  3. Yaping Qiu
  4. Zhen Gong
  5. Lei Deng
  6. Min Pan
  7. Huiping Yang
  8. Jianan Xu
  9. Li Yang
  10. Jin Li

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

COVID-19 is a highly contagious disease caused by a novel coronavirus SARS-CoV-2. The interaction between SARS-CoV-2 spike protein and the host cell surface receptor ACE2 is responsible for mediating SARS-CoV-2 infection. By analyzing the spike-hACE2 interacting surface, we predicted many hot spot residues that make major contributions to the binding affinity. Mutations on most of these residues are likely to be deleterious, leading to less infectious virus strains that may suffer from negative selection. Meanwhile, several residues with mostly advantageous mutations have been predicted. It is more probable that mutations on these residues increase the transmission ability of the virus by enhancing spike-hACE2 interaction. So far, only a limited number of mutations has been reported in this region. However, the list of hot spot residues with predicted downstream effects from this study can still serve as a tracking list for SARS-CoV-2 evolution studies. Coincidentally, one advantageous mutation, p.476G>S, started to surge in the last couple of weeks based on the data submitted to the public domain, indicating that virus strains with increased transmission ability may have already spread.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.05.04.077842: (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 analysis was performed using PyMol [31] (version 2.3.0) and Residue Scanning module of BioLuminate [32, 33] from Schrödinger suite.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    BioLuminate
    suggested: None
    Sequences for SARS-CoV and MERS-CoV were queried from NCBI virus database [35] using the blastn function implemented in BLAST V2.6.0 [36] with their reference genomes (SARS-CoV: NC_004718.3; MERS-CoV: NC_019843.3), respectively.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    For sequence variation and evolution analysis, we firstly performed multiple alignment at genome levels within each species using MAFFT V7.455 [37].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The domain information of SARS-CoV-2 spike protein (NCBI accession ID: YP_009724390.1) was determined using Pfam [40] via sequence search.
    Pfam
    suggested: (Pfam, RRID:SCR_004726)

    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.
    • No funding statement was detected.
    • 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 10.1101/2020.05.04.077842v1 on bioRxiv