On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with Special Focus on Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

  1. E.V. Mavrodiev
  2. M.L. Tursky
  3. N.E. Mavrodiev
  4. L. Schroder
  5. A.P. Laktionov
  6. M.C. Ebach
  7. D.M. Williams

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category “virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.

Article activity feed

  1. Version published to 10.17537/2022.17.289
  2. Version published to 10.1101/2020.10.17.343749v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.10.17.343749: (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
    Matrices and trees: All genomic alignments have been performed using MAFFT (13, 14, 15) following FFT-NS-I strategy with the command: mafft --inputorder --adjustdirection -- anysymbol --kimura 1 --maxiterate 1000 --6merpair input.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Manipulations with either the molecular or binary matrices and the tree-files have been performed with Mesquite v.
    Mesquite
    suggested: (Mesquite, RRID:SCR_017994)
    3.51 (22), PAUP* v. 4.0a (23) and FigTree v.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.10.17.343749v1 on bioRxiv