Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant

  1. Wentai Ma
  2. Jing Yang
  3. Haoyi Fu
  4. Chao Su
  5. Caixia Yu
  6. Qihui Wang
  7. Ana Tereza Ribeiro de Vasconcelos
  8. Georgii A. Bazykin
  9. Yiming Bao
  10. Mingkun Li

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Abstract

A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (median: 62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of these mutations were rarely observed in public databases and had a low mutation rate. In addition, the linkage disequilibrium between these mutations was low, with a limited number of mutations concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner.

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  1. Version published to 10.1016/j.gpb.2022.01.001
  2. ScreenIT

    SciScore for 10.1101/2022.01.05.474231: (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
    Identification of epitope regions on the Spike Protein: We downloaded the structures of 182 protein complexes of antibodies that bound to the SARS-CoV-2 Spike or its receptor-binding domain (RBD) or N-terminal domain (NTD) from the Protein Data Bank (all structures available before August 8, 2021, www.rcsb.org).
    N-terminal domain (NTD
    suggested: (Leinco Technologies Cat# LT2000, RRID:AB_2893936)
    Software and Algorithms
    SentencesResources
    Data collection: The sequencing data were retrieved from SRA database in NCBI (BioProject: PRJNA784038), which was generated by the Network for Genomic Surveillance in South Africa (NGS-SA) [2,6].
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Quality control and mutation detection: Quality control and adaptor trimming were performed by FASTP [30].
    FASTP
    suggested: (fastp, RRID:SCR_016962)
    The mpileup file and the read count file were generated by SAMtools [32] and Varscan2 [33].
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Phylogenetic construction was performed by IQ-TREE (1.6.12) [35].
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    TMRCA estimation: The estimation of the time to the most recent common ancestor (TMRCA) and mutation rate was performed by BEAST (2.6.4) [36] using 108 sequences collected between November 13, 2021, and November 23, 2021.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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 10.1101/2022.01.05.474231v1 on bioRxiv