Introductions and early spread of SARS-CoV-2 in France
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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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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 Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources 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. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)We then used SAMtools v1.3 to sort the aligned bam files and generate alignment statistics (WysokerA, RuanJ et al.) SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Aligned reads were manually inspected using … 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 Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources 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. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)We then used SAMtools v1.3 to sort the aligned bam files and generate alignment statistics (WysokerA, RuanJ et al.) SAMtoolssuggested: (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). MAFFTsuggested: (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-TREEsuggested: (IQ-TREE, RRID:SCR_017254)We checked for temporal signal using Tempest v1.5.3 (Rambaut, Lam et al. 2016). Tempestsuggested: (TempEst, RRID:SCR_017304)The time and divergence trees were visualized with FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/). FigTreesuggested: (FigTree, RRID:SCR_008515)Adobe Illustrator 2020 was used to prepare final tree figures. Adobe Illustratorsuggested: (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.
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