Estimating dates of origin and end of COVID-19 epidemics
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SciScore for 10.1101/2021.01.19.21250080: (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 Parameter inference with maximum likelihood was performed using the Powell algorithm implemented by Scipy.minimize function in Python. Scipysuggested: (SciPy, RRID:SCR_008058)Pythonsuggested: (IPython, RRID:SCR_001658)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:There are several limitations to this work. First, the serial interval ω and the time from infection to …
SciScore for 10.1101/2021.01.19.21250080: (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 Parameter inference with maximum likelihood was performed using the Powell algorithm implemented by Scipy.minimize function in Python. Scipysuggested: (SciPy, RRID:SCR_008058)Pythonsuggested: (IPython, RRID:SCR_001658)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:There are several limitations to this work. First, the serial interval ω and the time from infection to death θ, are largely unknown in France, as well as in many countries. Most of the known serial interval estimates rely on contact tracing data from Asia [14, 16], which could be slightly different from the distribution in France, due to different contact structure, or different non-pharmaceutical measures applied. Obviously, the serial interval distribution has a strong impact on the dynamics. We do show however in Figure S3 that the variance of this interval does not have a strong impact on the results. Another important limitation about the estimation of the date of origin of the epidemic comes from the assumption that only one initial infected person caused the epidemic. Clearly, most epidemics outside China were seeded by multiple importation events. The problem is that there is an identifiability issue because it is impossible to estimate both the number of initial infected cases and the time to threshold of 100 deaths with incidence data only. However, some estimates made in the UK from phylogenetic data as well as the combination of prevalence and travel data show that the estimated number of importation events is less than 5 per day before the end of February, when the virus was beginning to circulate at higher levels throughout Europe [19]. Assuming that the dynamic was similar in France, we could verify that the dynamic was only sensitive to the importation events...
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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