δ1 variant of SARS-COV-2 acquires spike V1176F and yields a highly mutated subvariant in Europe

  1. Xiang-Jiao Yang

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Abstract

Genomic surveillance of SARS-COV-2 has revealed that in addition to many variants of interests, this virus has yielded four variants of concern, α, β, γ and δ, as designated by the World Health Organization. δ variant has recently become the predominant pandemic driver around the world and yielded four different subvariants (δ1, δ2, δ3 and δ4). Among them, δ1 has emerged as the key subvariant that drives the pandemic in India, Europe and the USA. A relevant question is whether δ1 subvariant continues to evolve and acquires additional mutations. Related to this, this subvariant has acquired spike V1176F, a signature substitution of γ variant, and yielded a new sublineage, δ1F. The substitution alters heptad repeat 2 of spike protein and is expected to improve interaction with heptad repeat 1 and enhance virus entry. Moreover, there are δ1F sublineages encoding spike N501Y, A783S, Q836E and V1264L. While N501Y is a signature substitution shared by α, β and γ variants, V1264L is a key substitution in a δ1 sublineage that is a major pandemic driver in Southeast Asia. The Q836E-encoding lineage carries an average of 50 mutations per genome, making it the most mutated variant identified so far. Similar to δ1 subvariant, δ2 subvariant has also acquired spike V1176F and yielded new sublineages. Together, these results suggest that V1176F is a recurrent spike substitution that is frequently acquired by SARS-COV-2 variants to improve viral fitness. It is thus important to track the evolutionary trajectory of related variants for considering and instituting the most effective public health measures.

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    SciScore for 10.1101/2021.10.16.463825: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The cleaned Fasta file was also uploaded onto SnapGene (version 5.3.2) for multisequence alignment via the MAFFT tool.
    SnapGene
    suggested: (SnapGene, RRID:SCR_015052)
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    PyMol structural modeling: The PyMol molecular graphics system (version 2.4.2, https://pymol.org/2/) from Schrödinger, Inc. was used for downloading structure files from the PDB database for further analysis and image generation.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    Structural images were cropped via Adobe Photoshop for further presentation through Illustrator.
    Adobe Photoshop
    suggested: (Adobe Photoshop, RRID:SCR_014199)

    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.
    • 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 10.1101/2021.10.16.463825v2 on bioRxiv
  3. Version published to 10.1101/2021.10.16.463825v1 on bioRxiv