Adaptive Time-Dependent Priors and Bayesian Inference to Evaluate SARS-CoV-2 Public Health Measures Validated on 31 Countries
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Abstract
With the rapid spread of the SARS-CoV-2 virus since the end of 2019, public health confinement measures to contain the propagation of the pandemic have been implemented. Our method to estimate the reproduction number using Bayesian inference with time-dependent priors enhances previous approaches by considering a dynamic prior continuously updated as restrictive measures and comportments within the society evolve. In addition, to allow direct comparison between reproduction number and introduction of public health measures in a specific country, the infection dates are inferred from daily confirmed cases and confirmed death. The evolution of this reproduction number in combination with the stringency index is analyzed on 31 European countries. We show that most countries required tough state interventions with a stringency index equal to 79.6 out of 100 to reduce their reproduction number below one and control the progression of the pandemic. In addition, we show a direct correlation between the time taken to introduce restrictive measures and the time required to contain the spread of the pandemic with a median time of 8 days. This analysis is validated by comparing the excess deaths and the time taken to implement restrictive measures. Our analysis reinforces the importance of having a fast response with a coherent and comprehensive set of confinement measures to control the pandemic. Only restrictions or combinations of those have shown to effectively control the pandemic.
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SciScore for 10.1101/2020.06.10.20126870: (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
No key resources detected.
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:One limitation of the dataset used in this analysis is that it does not measure whether people have to wear mask either in public transport or in all closed environments. It would be important to include those data as more countries are introducing this type of measures to prevent the resurgence of the virus. Our analysis also looked at …
SciScore for 10.1101/2020.06.10.20126870: (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
No key resources detected.
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:One limitation of the dataset used in this analysis is that it does not measure whether people have to wear mask either in public transport or in all closed environments. It would be important to include those data as more countries are introducing this type of measures to prevent the resurgence of the virus. Our analysis also looked at the timing of the NPIs introduction. We found that there is a strong correlation (Pearson coefficient of 0.762) between the time at which NPIs were introduced and the time at which a country managed to control the epidemic with a reproductive number reducing below one. The United Kingdom can serve as an interesting example. The UK had initially planned to build “targeted herd immunity” delaying the introduction of restrictive measure. As a result of this delay, the UK were only able to contain the epidemic 30 days after the fifth death occurred in the country when the median time for the countries included in our analysis was of eight days. There are three outliers in our analysis being Andorra, Sweden and Iceland. Sweden has decided not to introduce a complete lockdown and stands with one of the highest daily death incidence in Europe (May 23rd : Sweden - 5.34 deaths per million people per day; other European countries analyzed 0.82 on the same day 25). A drawback of considering the evolution in the different countries at a national level and not at a regional one is that the heterogeneity of the spread of the virus is disregarded. To evaluat...
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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