Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

  1. Saif M. Khodary
  2. Ali Mostafa Anwar

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens . Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.

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  1. Version published to 10.1101/2020.04.01.019463v3 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2020.04.01.019463: (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
    The frequencies of tRNAs of Homo sapiens was obtained from the GtRNAdb (http://gtrnadb.ucsc.edu/) (Chan and Lowe, 2009).
    http://gtrnadb.ucsc.edu/
    suggested: (GtRNAdb - Genomic tRNA Database, RRID:SCR_006939)
    Different R packages as vhcub, SeqinR, ggplot2 and stats (Anwar et al., 2020; Charif and Lobry, 2007; R Core Team, 2018;
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    As well as a python package named CAI (Lee, 2018) was used to estimate the CAI for the tested viral isolates.
    python
    suggested: (IPython, RRID:SCR_001658)
    Multiple sequence alignments for the whole genome of the 13 SARS-CoV-2 was done with MAFFT software (v7.450) and the phylogenetic analysis was performed with MEGA-X software (v10.1).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    MEGA-X
    suggested: None

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  3. Version published to 10.1101/2020.04.01.019463v2 on bioRxiv
  4. Version published to 10.1101/2020.04.01.019463v1 on bioRxiv