Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization

  1. Lukas Zemaitis
  2. Gediminas Alzbutas
  3. Dovydas Gecys
  4. Arnoldas Pautienius
  5. Rasa Ugenskiene
  6. Marius Sukys
  7. Vaiva Lesauskaite

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Abstract

Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April–May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods.

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  1. Version published to 10.3390/microorganisms10071356
  2. ScreenIT

    SciScore for 10.1101/2021.11.21.21266655: (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

    Antibodies
    SentencesResources
    Antibody escape effect estimation: Two S protein sequence variants 156_158del (B.1.1.523 lineage) and 156_157del & R158G (delta variant) were modelled using Rosetta package (2021.16.61629_bundle)31.
    R158G
    suggested: None
    Software and Algorithms
    SentencesResources
    The tree was build using IQ-TREE with 2.1.2 General time reversible model with unequal rates and unequal base frequencies were used21 allowing for a proportion of invariable sites together with discrete Gamma model22.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    The set of sequences collected as described above were clustered into transmission clusters using Phydelity v2.0 [https://github.com/alvinxhan/Phydelity]23.
    Phydelity
    suggested: None
    Sequences were further clustered into identical sequence clusters using CD-HIT v4.8.1
    CD-HIT
    suggested: (CD-HIT, RRID:SCR_007105)
    The resulting tree was analysed detected potential changes in the haplotypes was done using a custom script written in julia 1.6 exploiting capabilities of the NewickTree library [https://github.com/arzwa/NewickTree.jl].
    NewickTree
    suggested: None
    The detection of recombination events at DNA level was done using PoSeiDon workflow27 [https://github.com/hoelzer/poseidon cloned at 2021 09 28] that runs GARD program to identify recombination events28.
    GARD
    suggested: (Genetic and Rare Diseases Information Center, RRID:SCR_008695)
    The mutations into the complexes were introduced by consecutively applying FoldX command: RepairPDB, BuildModel, AnalyseComplex.
    FoldX
    suggested: (FoldX, RRID:SCR_008522)

    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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  3. Version published to 10.1101/2021.11.21.21266655v1 on medRxiv