Introductions and early spread of SARS-CoV-2 in France

  1. Fabiana Gámbaro
  2. Sylvie Behillil
  3. Artem Baidaliuk
  4. Flora Donati
  5. Mélanie Albert
  6. Andreea Alexandru
  7. Maud Vanpeene
  8. Méline Bizard
  9. Angela Brisebarre
  10. Marion Barbet
  11. Fawzi Derrar
  12. Sylvie van der Werf
  13. Vincent Enouf
  14. Etienne Simon-Loriere

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Abstract

Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.24.059576: (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

    Software and Algorithms
    SentencesResources
    Genome assembly: Raw reads were trimmed using Trimmomatic v0.36 (Bolger, Lohse et al. 2014) to remove Illumina adaptors and low quality reads, as well as primer sequences for samples sequenced with the amplicon-based approach.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    We then used SAMtools v1.3 to sort the aligned bam files and generate alignment statistics (WysokerA, RuanJ et al.)
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Aligned reads were manually inspected using Geneious prime v2020.1.2 (2020) (https://www.geneious.com/), and consensus sequences were generated using a minimum of 3X read-depth coverage to make a base call.
    https://www.geneious.com/
    suggested: (Geneious, RRID:SCR_010519)
    Within the pipeline, sequences were aligned to the reference Wuhan/Hu-1/2020 strain of SARS-CoV-2 (GenBank accession MN908947) using MAFFT v7.455 (Katoh and Toh 2010).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A maximum likelihood phylogenetic tree was built using IQ-TREE v1.5.5 with the GTR model (Kalyaanamoorthy, Minh et al. 2017), after masking 130 and 50 nucleotides from the 5’ and 3’ ends of the alignment, respectively, as well as single nucleotides at positions 18529, 29849, 29851, 29853 as normally set in Nextstrain implementation for SARS-CoV-2.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    We checked for temporal signal using Tempest v1.5.3 (Rambaut, Lam et al. 2016).
    Tempest
    suggested: (TempEst, RRID:SCR_017304)
    The time and divergence trees were visualized with FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Adobe Illustrator 2020 was used to prepare final tree figures.
    Adobe Illustrator
    suggested: (Adobe Illustrator, RRID:SCR_010279)

    Results from OddPub: Thank you for sharing your code.

    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.
    • 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 10.1101/2020.04.24.059576v2 on bioRxiv
  3. Version published to 10.1101/2020.04.24.059576v1 on bioRxiv