A snapshot of SARS-CoV-2 genome availability up to 30 th March, 2020 and its implications

  1. Carla Mavian
  2. Simone Marini
  3. Mattia Prosperi
  4. Marco Salemi

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Abstract

The SARS-CoV-2 pandemic has been growing exponentially, affecting nearly 900 thousand people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published, in scientific journals as well as through non-peer reviewed channels, to investigate SARS-CoV-2 genetic heterogeneity and spatiotemporal dissemination. We examined full genome sequences currently available to assess the presence of sufficient information for reliable phylogenetic and phylogeographic studies in countries with the highest toll of confirmed cases. Although number of-available full-genomes is growing daily, and the full dataset contains sufficient phylogenetic information that would allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 datasets still present severe limitations. Studies assessing within country spread or transmission clusters should be considered preliminary at best, or hypothesis generating. Hence the need for continuing concerted efforts to increase number and quality of the sequences required for robust tracing of the epidemic.

Significance Statement

Although genome sequences of SARS-CoV-2 are growing daily and contain sufficient phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution.

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    SciScore for 10.1101/2020.04.01.020594: (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
    Confirmed cases were retrieved from the March 29th data of the Covid19 website provided by Johns Hopkins University (16).
    Covid19
    suggested: None
    Evaluation of the presence of phylogenetic signal satisfying resolved phylogenetic relationships among sequences was carried out with IQ-TREE, allowing the software to search for all possible quartets using the best-fitting nucleotide substitution model (11).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Exploration of temporal structure, i.e. presence of molecular clock in the data, was assessed by regression of divergence -root-to-tip genetic distance-against sampling time using TempEst (13).
    TempEst
    suggested: (TempEst, RRID:SCR_017304)

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

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  2. Version published to 10.1101/2020.04.01.020594v1 on bioRxiv