Synonymous sites in SARS-CoV-2 genes display trends affecting translational efficiency

  1. Qingsheng Huang
  2. Huan Gao
  3. Lingling Zheng
  4. Xiujuan Chen
  5. Shuai Huang
  6. Huiying Liang

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Abstract

A novel coronavirus, SARS-CoV-2, has caused a pandemic of COVID-19. The evolutionary trend of the virus genome may have implications for infection control policy but remains obscure. We introduce an estimation of fold change of translational efficiency based on synonymous variant sites to characterize the adaptation of the virus to hosts. The increased translational efficiency of the M and N genes suggests that the population of SARS-CoV-2 benefits from mutations toward favored codons, while the ORF1ab gene has slightly decreased the translational efficiency. In the coding region of the ORF1ab gene upstream of the −1 frameshift site, the decreasing of the translational efficiency has been weakening parallel to the growth of the epidemic, indicating inhibition of synthesis of RNA-dependent RNA polymerase and promotion of replication of the genome. Such an evolutionary trend suggests that multiple infections increased virulence in the absence of social distancing.

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    SciScore for 10.1101/2020.05.30.125740: (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
    A dataset of single-cell transcriptome of human lung tissue (GEO: GSE122960)(27) was re-analysis with R package Seurat version 3.1.4(28) following a previous study(15).
    Seurat
    suggested: (SEURAT, RRID:SCR_007322)
    The corresponding transcript sequences were obtained from GENCODE version 26(31).
    GENCODE
    suggested: (GENCODE, RRID:SCR_014966)
    A multiple sequence alignment (MSA) of 516 genome sequences (sequences of more than 29000 nt) was built using MUSCLE version 3.8.31(32) with default setting.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    A maximum likelihood phylogenetic tree of the 317 sequences was built using RAxML-NG version 0.9.0(33) with GTR+G substitution model and bootstrapping with MRE-based convergence criterion up to 1000 replicates.
    RAxML-NG
    suggested: None

    Results from OddPub: Thank you for sharing your data.

    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.

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  2. Version published to 10.1101/2020.05.30.125740v1 on bioRxiv