Direct RNA sequencing and early evolution of SARS-CoV-2

  1. George Taiaroa
  2. Daniel Rawlinson
  3. Leo Featherstone
  4. Miranda Pitt
  5. Leon Caly
  6. Julian Druce
  7. Damian Purcell
  8. Leigh Harty
  9. Thomas Tran
  10. Jason Roberts
  11. Nichollas Scott
  12. Mike Catton
  13. Deborah Williamson
  14. Lachlan Coin
  15. Sebastian Duchene

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Abstract

Fundamental aspects of SARS-CoV-2 biology remain to be described, having the potential to provide insight to the response effort for this high-priority pathogen. Here we describe the first native RNA sequence of SARS-CoV-2, detailing the coronaviral transcriptome and epitranscriptome, and share these data publicly. A data-driven inference of viral genetic features and evolutionary rate is also made. The rapid sharing of sequence information throughout the SARS-CoV-2 pandemic represents an inflection point for public health and genomic epidemiology, providing early insights into the biology and evolution of this emerging pathogen.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.05.976167: (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
    Both signal-space and basecalled read data are available at BioProject PRJNA608224.
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Subgenome bins were re-aligned, with coverage calculated in SAMtools [M4], and plotted using ggplot2 [M5] in R [M6].
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Assessment of publicly available proteomes: Proteomic datasets were downloaded from the PRIDE proteomic database [M11] (Pride accession: PXD017710) and processes using Maxquant (1.6.3.4 [M12]) allowing semi-specific free-N-terminus tryptic as a protease specificity.
    PRIDE
    suggested: (Pride-asap, RRID:SCR_012052)
    SARS-CoV-2 Phylogenetics: In order to estimate the evolutionary rate and time of origin of SARS-CoV-2, we carried out phylogenetic analyses in BEAST v1.101 [M13 on three datasets.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.03.05.976167v2 on bioRxiv
  3. Version published to 10.1101/2020.03.05.976167v1 on bioRxiv