Early phylodynamics analysis of the COVID-19 epidemic in France
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SciScore for 10.1101/2020.06.03.20119925: (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 Sentences Resources Sequences were aligned and cleaned using the Augur pipeline developed by nextstrain (Hadfield et al., 2018). Augursuggested: NonePhylogenetic inference: We first performed a maximum likelihood inference ofthe phylogeny using SMS (Lefort et al., 2017) and PhyML (Guindon and Gascuel, 2003). PhyMLsuggested: (PhyML, RRID:SCR_014629)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: We detected the following sentences addressing limitations in the …SciScore for 10.1101/2020.06.03.20119925: (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 Sentences Resources Sequences were aligned and cleaned using the Augur pipeline developed by nextstrain (Hadfield et al., 2018). Augursuggested: NonePhylogenetic inference: We first performed a maximum likelihood inference ofthe phylogeny using SMS (Lefort et al., 2017) and PhyML (Guindon and Gascuel, 2003). PhyMLsuggested: (PhyML, RRID:SCR_014629)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: We detected the following sentences addressing limitations in the study:Before summarizing the results, we prefer to point out several limitations of our analysis. First, the French clade we analysed is in fact an international clade: although most French sequences appear to be grouping into two main subclades within this clade, it is possible that the variations in epidemic growth that we detect are more due to European than French control policies. Second, some French regions (e.g. Auvergne-Rhone-Alpes) are more represented than others (e.g. Occitanie is absent), which could bias the analysis at the national level. However, the coverage is largely proportional to the state of the epidemics in France in March, where the Paris area and the East of France were more heavily impacted. Therefore, we expect the addition of sequences from less impacted regions to have a limited effect on our doubling time and reproduction number estimates. Finally, the molecular clock had to be set in this analysis because we do not have enough samples from the month of Feb in France. Despite these limitations, our results obtained early Apr confirm a slowing down of the epidemic in France, where the epidemic peak in terms of ICU admissions was reached on Apr 1. Indeed, by adding sequences sampled between Mar 12 and 24 to the phylogeny, the doubling time of the epidemic estimated by an exponential growth coalescent model increased by 48%. This slowdown is more clearly detected using a birth death model via the temporal reproduction number ℛ(t): the median value decreas...
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.
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- No protocol registration statement was detected.
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