Infection Groups Differential (IGD) Score Reveals Infection Ability Difference between SARS-CoV-2 and Other Coronaviruses

  1. Ziwei Song
  2. Xingchen Zhou
  3. Yuanyuan Cai
  4. Shuo Feng
  5. Tingting Zhang
  6. Yun Wang
  7. Maode Lai
  8. Jing Li

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Abstract

The Corona Virus Disease 2019 (COVID-19) pandemic that began in late December 2019 has resulted in millions of cases diagnosed worldwide. Reports have shown that SARS-CoV-2 shows extremely higher infection rates than other coronaviruses. This study conducted a phylogenetics analysis of 91 representative coronaviruses and found that the functional spike protein of SARS-CoV-2, which interacts with the human receptor ACE2, is actually not undergoing distinct selection pressure compared to other coronaviruses. Furthermore, we define a new measurement, infection group differential (IGD) score, in assessing the infection ability of two human coronavirus groups. There are nine extremely high IGD (ehIGD) sites in the receptor-binding domain (RBD) out of 40 high IGD (hIGD) sites that exhibit a unique infection-related pattern from the haplotype network and docking energy comparison. These 40 hIGD sites are basically conserved among the SARS-CoV-2, i.e. there are only two hIGD sites mutated in four out of 1,058 samples, defined as rare-mutation hIGD (rhIGD) sites. In conclusion, ehIGD and rhIGD sites might be of great significance to the development of vaccines.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.12.090324: (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
    Homologous sequence searching of SARS-like coronaviruses spike protein was first performed by BLASTP (v 2.2.29+) [14] in NR (Non-Redundant Protein Sequence Database), and 868 sequences were selected under the condition of sequence length > 600 aa and a sequence identity > 30%.
    BLASTP
    suggested: (BLASTP, RRID:SCR_001010)
    Phylogenetic analysis: The DNA sequences of whole genome and related protein sequences of 91 coronaviruses were aligned using mafft v7.455 [15], and the result multiple sequence was trimmed for poorly aligned positions with Gblock 0.91b [16].
    mafft
    suggested: (MAFFT, RRID:SCR_011811)
    RAxML v8.2.12 [17] was used to build the maximum likelihood phylogenetic tree of genomes with the parameters “-m GTRCAT” and protein with the parameters “-m PROTGAMMAILGX”.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    Codon usage bias analysis: Condonw v1.3 [19] was used to calculate the universal index value of each codon of the Cds of coronavirus functional protein.
    Condonw
    suggested: None
    Ka/Ks analysis: Ka/KS ratios were calculated using KaKs_Calculator 2.0 [20] and used in the analysis of selection pressure.
    KaKs_Calculator
    suggested: None
    Haplotype network analysis: DnaSP v6.12.03 [21] was used to generate multi-sequence aligned haplotype data.
    DnaSP
    suggested: (DnaSP, RRID:SCR_003067)
    Arlequin v3.5.2.2 [22] was used to estimate haplotype frequency.
    Arlequin
    suggested: (ARLEQUIN, RRID:SCR_009051)

    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.

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  2. Version published to 10.1101/2020.05.12.090324 on bioRxiv