Phylogenetic analysis and in silico studies link spike Q675H mutation to SARS-CoV-2 adaptive evolution

  1. Bertelli Anna
  2. D’Ursi Pasqualina
  3. Campisi Giovanni
  4. Messali Serena
  5. Milanesi Maria
  6. Giovanetti Marta
  7. Ciccozzi Massimo
  8. Caccuri Francesca
  9. Caruso Arnaldo

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Abstract

Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region delimiting the conformational space of the highly flexible loop containing the furin cleavage site. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was found to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation is likely to confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we show an ongoing increase in the occurrence of Q675H spike mutation in the most common SARS-CoV-2 variants of concern (VOC). This finding highlights that, VOC are still evolving and start acquiring the Q675H mutation. At the same time, it suggests that our hypothesis of fitness advantage prompted by Q675H could be concrete.

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    SciScore for 10.1101/2021.10.27.466055: (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
    Pooled libraries were subsequently loaded in a 300-cycle sequencing cartridge and deep se-quencing was performed on an Illumina MiSeq platform
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Sequencing raw data were checked for quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then analyzed with the specifically designed software SOPHiA GENETICS’ SARS-CoV-2 Panel (SOPHiA GENETICS, Lausanne, Switzerland)
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Whole genome sequences were aligned with MAFFT (FF-NS-2 algorithm) using default parameters [33].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The alignment was manually curated with Aliview [34] to remove artifacts at the ends and within the alignment.
    Aliview
    suggested: (AliView, RRID:SCR_002780)
    Pymol mutagenesis wizard was used to model Q675H and D614G for both wild-type (wt) and mutant systems [36].
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    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.

    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.
    • 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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  2. Version published to 10.1101/2021.10.27.466055v1 on bioRxiv