Insertions in the SARS-CoV-2 Spike N-Terminal Domain May Aid COVID-19 Transmission

  1. Su Datt Lam
  2. Vaishali P Waman
  3. Christine Orengo
  4. Jonathan Lees

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Abstract

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged which may affect transmissibility, disease severity and re-infection risk. Most studies focus on the receptor-binding domain (RBD) of the Spike protein. However, some studies suggest that the Spike N-terminal domain (NTD) may have a role in facilitating virus entry via sialic-acid receptor binding. Furthermore, most VOCs include novel NTD variants. Recent analyses demonstrated that NTD insertions in VOCs tend to lie close to loop regions likely to be involved in binding sialic acids. We extended the structural characterisation of these putative sugar binding pockets and explored whether variants could enhance the binding to sialic acids and therefore to the host membrane, thereby contributing to increased transmissibility. We found that recent NTD insertions in VOCs (i.e., Gamma, Delta and Omicron variants) and emerging variants of interest (VOIs) (i.e., Iota, Lambda, Theta variants) frequently lie close to known and putative sugar-binding pockets. For some variants, including the recent Omicron VOC, we find increases in predicted sialic acid binding energy, compared to the original SARS-CoV-2, which may contribute to increased transmission. We examined the similarity of NTD across a range of related Betacoronaviruses to determine whether the putative sugar-binding pockets are sufficiently similar to be exploited in drug design. Despite global sequence and structure similarity, most sialic-acid binding pockets of NTD vary across related coronaviruses. Typically, SARS-CoV-2 possesses additional loops in these pockets that increase contact with polysaccharides. Our work suggests ongoing evolutionary tuning of the sugar-binding pockets in the virus. Whilst three of the pockets are too structurally variable to be amenable to pan Betacoronavirus drug design, we detected a fourth pocket that is highly structurally conserved and could therefore be investigated in pursuit of a generic drug. Our structure-based analyses help rationalise the effects of VOCs and provide hypotheses for experiments. For example, the Omicron variant, which has increased binding to sialic acids in pocket 3, has a rather unique insertion near pocket 3. Our work suggests a strong need for experimental monitoring of VOC changes in NTD.

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    SciScore for 10.1101/2021.12.06.471394: (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
    We extracted the Spike protein sequences by scanning the sequence of the SARS-CoV-2 Spike protein (YP_009724390.1) against the nucleotide database of BCoV sequences using NCBI BLAST v2.6 tblastn (Altschul et al., 1990).
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    FunMOD generated query–template alignments using HH-suite version 3 (Steinegger et al., 2019), which were then used as input to the MODELLER v.
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    The evolutionary history was inferred using the Maximum Likelihood method and the analyses were conducted using MEGA X (Kumar et al., 2018).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Protein structures were rendered using PyMOL (Schrödinger and DeLano, 2020) and UCSF Chimera (Pettersen et al., 2004).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    The sialic acid used was 9-O-acetylated sialic acid (PubChem ID 71312953).
    PubChem
    suggested: (PubChem, RRID:SCR_004284)

    Results from OddPub: Thank you for sharing your code.

    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.

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    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 8. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    Results from scite Reference Check: We found no unreliable references.

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