Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea

  1. Ha Nui Kim
  2. Soo-Young Yoon
  3. Chae Seung Lim
  4. Chang Kyu Lee
  5. Jung Yoon

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Abstract

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  1. Version published to 10.1016/j.jcv.2022.105213
  2. ScreenIT

    SciScore for 10.1101/2022.03.15.484550: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: This study was approved by the Institutional Review Board (IRB) of the Korea University Guro Hospital (IRB number:
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Multiple sequence alignment was performed using the nucleotide sequences of the HN gene obtained in this study with those of the reference strains, using the MUSCLE algorithm (16) implemented in MEGA X software (17).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    MEGA X
    suggested: None
    The best-fit substitution model was determined using ModelFinder with TIM+F+I+G4 based on the minimum Bayesian information criterion value (19).
    ModelFinder
    suggested: None
    The best model among the six clock-tree model combinations, the relaxed clock log-normal and constant coalescent population, was chosen by path sampling and stepping stone, using the model-selection package implemented in BEAST.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The Tracer program v1.7.1 (20) was used to ensure that the effective sample size was greater than 200 for all the parameters.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    The maximum clade credibility tree information was summarized using TreeAnnotator v2.6.6 (21) after burning in 10% of the trees.
    TreeAnnotator
    suggested: (BEAST2, RRID:SCR_017307)
    The Bayesian MCMC phylogenetic tree was visualized using FigTree v1.4.4 (22).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Amino acid sequence analysis: The amino acid sequences were obtained by translating the nucleotide sequences of the partial nucleotide sequence of the HN gene using the standard genetic code in MEGA X.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The crystal structure of HN protein was visualized using PyMOL 2.0 (24), based on the previously published crystal structure of HN (PDB ID: 1V3B).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Entropy analysis by Shannon entropy plot was performed using BioEdit, with a threshold value of 0.2 (25). 2.5.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    Selection pressure analysis: The selection pressure on the HN gene of HPIV3 was estimated using the Datamonkey server (http://www.datamonky.org/).
    Datamonkey server
    suggested: (DataMonkey, RRID:SCR_010278)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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.

  3. Version published to 10.1101/2022.03.15.484550v1 on bioRxiv