VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

  1. Daniele Ramazzotti
  2. Fabrizio Angaroni
  3. Davide Maspero
  4. Carlo Gambacorti-Passerini
  5. Marco Antoniotti
  6. Alex Graudenzi
  7. Rocco Piazza

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  1. ScreenIT

    SciScore for 10.1101/2020.04.22.044404: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    On the one hand, the probabilistic framework underlying VERSO STEP #1 delivers highly accurate and robust phylogenetic models from clonal variants, also in condition of noisy observations and sampling limitations, as proven by extensive simulations and by the application to two-large scale SARS-CoV-2 datasets generated from distinct sequencing platforms. On the other hand, the characterization of intra-host genomic diversity provided by VERSO STEP #2 allows one to identify undetected infection paths, which were in our case validated with contact tracing data, as well as to intercept variants involved in homoplasies. This may represents a major advancement in the analysis of viral evolution and spread and should be quickly implemented in combination to data-driven epidemiological models, to deliver a high-precision platform for pathogen detection and surveillance12,99. This might be particularly relevant for countries which suffered outbreaks of exceptional proportions and for which the limitations and inhomogeneity of diagnostic tests have proved insufficient to define reliable descriptive/predictive models of disease diffusion. For instance, it was hypothesized that the rapid diffusion of COVID-19 might be likely due to the extremely high number of untested asymptomatic hosts100. More accurate and robust phylogenetic models may allow one to improve the assessment of molecular clocks and, accordingly, the estimation of the parameters of epidemiological models such as SIR and ...

    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.

    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.

  2. Version published to 10.1016/j.patter.2021.100212
  3. Version published to 10.1101/2020.04.22.044404v4 on bioRxiv
  4. Version published to 10.1101/2020.04.22.044404v3 on bioRxiv
  5. Version published to 10.1101/2020.04.22.044404v2 on bioRxiv
  6. ScreenIT

    SciScore for 10.1101/2020.04.22.044404: (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
    Furthermore, we considered 4 additional samples from NCBI BioProject PRJNA607948 all obtained from one unique individual from Wisconsin, USA (1 swab and 3 independent passage isolates; Illumina MiSeq), which were used to validate the discovered minor variant g.
    BioProject
    suggested: (NCBI BioProject, SCR_004801)
    Following [43], we used Trimmomatic (version 0.39) to remove the nucleotides with low quality score from the RNA sequences with the following settings: LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:40.
    Trimmomatic
    suggested: (Trimmomatic, SCR_011848)
    We generated sorted BAM files from bwa mem results using SAMtools (version 1.10) and removed duplicates with Picard (version 2.22.2).
    SAMtools
    suggested: (SAMTOOLS, SCR_002105)
          <div style="margin-bottom:8px">
        <div><b>Picard</b></div>
        <div>suggested: (Picard, <a href="https://scicrunch.org/resources/Any/search?q=SCR_006525">SCR_006525</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Variant calling was performed generating mpileup files using SAMtools and then running VarScan (min-var-freq parameter set to 0.01) [44].</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>VarScan</b></div>
        <div>suggested: (VARSCAN, <a href="https://scicrunch.org/resources/Any/search?q=SCR_006849">SCR_006849</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We generated sorted BAM files from bwa mem results using SAMtools (version 1.10) and removed duplicates with Picard (version 2.22.2).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>SAMtools</b></div>
        <div>suggested: (SAMTOOLS, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002105">SCR_002105</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>Picard</b></div>
        <div>suggested: (Picard, <a href="https://scicrunch.org/resources/Any/search?q=SCR_006525">SCR_006525</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Standard phylogenomic analyses were also performed by applying MrBayes [22] to binarized VF profiles (default parameters, VF binarization threshold = 0.50) and Nexstrain-Augur [8] to consensus sequences of the 18 samples retrieved by GISAID (default parameters; the models are shown in the Suppl. Fig. 3 and 4.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>MrBayes</b></div>
        <div>suggested: (MrBayes, <a href="https://scicrunch.org/resources/Any/search?q=SCR_012067">SCR_012067</a>)</div>
      </div>
    </td></tr></table>

    Results from Barzooka: We also found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from OddPub: Thank you for sharing your code.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, please follow this link.

  7. Version published to 10.1101/2020.04.22.044404v1 on bioRxiv