Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans

  1. Xia Xue
  2. Jianxiang Shi
  3. Hongen Xu
  4. Yaping Qin
  5. Zengguang Yang
  6. Shuaisheng Feng
  7. Danhua Liu
  8. Liguo Jian
  9. Linlin Hua
  10. Yaohe Wang
  11. Qi Zhang
  12. Xueyong Huang
  13. Xiaoju Zhang
  14. Xinxin Li
  15. Chunguang Chen
  16. Jiancheng Guo
  17. Wenxue Tang
  18. Jianbo Liu

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Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus causing the COVID-19 pandemic in 2020. High adaptive plasticity on the spike protein of SASR-CoV-2 enables it to transmit across different host species. In the present study, we collected 2092 high-quality genome sequences of SARS-CoV-2 from 160 regions in over 50 countries and reconstructed their phylogeny. We also analyzed the polymorphic interaction between spike protein and human ACE2 (hACE2). Phylogenetic analysis of SARS-CoV-2 suggests that SARS-CoV-2 is probably originated from a recombination event on the spike protein between a bat coronavirus and a pangolin coronavirus that endows it humans infectivity. Compared with other regions in the S gene of SARS-CoV-2, the direct-binding sites of the receptor-binding domain (RBD) is more conserved. We focused on 3,860 amino acid mutations in spike protein RBD (T333-C525) of SARS-CoV-2 and simulated their differential stability and binding affinity to hACE2 (S19-D615). The results indicate no preference for SARS-CoV-2 infectivity on people of different ethnic groups. The variants in the spike protein of SARS-CoV-2 may also be a good indicator demonstrating the transmission route of SARS-CoV-2 from its natural reservoir to human hosts.

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  1. Version published to 10.1038/s41598-021-82938-2
  2. ScreenIT

    SciScore for 10.1101/2020.06.25.170704: (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 this study, all the virus sequences were aligned with Clustal Omega (V1.2.3)18 and filtered by sequences containing continuous 15 Ns, and 327 non-repetitive sequences of S gene and 469 of S, N, M, E combined sequences of SARS-CoV-2 were extracted from the filtered genome sequences respectively.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    We chose the maximum likelihood tree reconstructed using MEGA v5.220.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Figtree v1.421 was performed on editing and screening the evolutionary tree topology.
    Figtree
    suggested: (FigTree, RRID:SCR_008515)
    The genomic variants in the human ACE2 gene for different populations were downloaded from the gnomAD database (https://gnomad.broadinstitute.org/) The proposed residue sites were substituted to the amino acids that have the reported point mutations according to gnomAD.
    https://gnomad.broadinstitute.org/
    suggested: (Genome Aggregation Database, RRID:SCR_014964)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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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  3. Version published to 10.1101/2020.06.25.170704v1 on bioRxiv