Spatially resolved simulations of the spread of COVID-19 in three European countries
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Abstract
We explore the spatial and temporal spread of the novel SARS-CoV-2 virus under containment measures in three European countries based on fits to data of the early outbreak. Using data from Spain and Italy, we estimate an age dependent infection fatality ratio for SARS-CoV-2, as well as risks of hospitalization and intensive care admission. We use them in a model that simulates the dynamics of the virus using an age structured, spatially detailed agent based approach, that explicitly incorporates governmental interventions and changes in mobility and contact patterns occurred during the COVID-19 outbreak in each country. Our simulations reproduce several of the features of its spatio-temporal spread in the three countries studied. They show that containment measures combined with high density are responsible for the containment of cases within densely populated areas, and that spread to less densely populated areas occurred during the late stages of the first wave. The capability to reproduce observed features of the spatio-temporal dynamics of SARS-CoV-2 makes this model a potential candidate for forecasting the dynamics of SARS-CoV-2 in other settings, and we recommend its application in low and lower-middle income countries which remain understudied.
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SciScore for 10.1101/2020.11.25.20238600: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, the limitations of the radiation model are evident in the description of mobility in Spain that only scores a CPC of 0.21. Possibly, the use of more recent models for human mobility might mitigate such discrepancies [30]. The agreement of the R0 obtained from the independent fits performed in each country as well as the capability of the model of reproducing the observed data suggest its possible use in other contexts. One …
SciScore for 10.1101/2020.11.25.20238600: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, the limitations of the radiation model are evident in the description of mobility in Spain that only scores a CPC of 0.21. Possibly, the use of more recent models for human mobility might mitigate such discrepancies [30]. The agreement of the R0 obtained from the independent fits performed in each country as well as the capability of the model of reproducing the observed data suggest its possible use in other contexts. One possibility could be to estimate the impact of future interventions in the countries studied in this work or other European countries, provided age-stratified information on cases and deaths from COVID-19 as well as information on the mobility of individuals are available for such countries. Another possibility could be its use in Low and Middle income countries: the key ingredients that would permit this are the availability of contact matrices from the work of Prem et al. [22] for almost all countries worldwide, the assumption that age-dependent susceptibility does not depend on anything other than age, and similarly the assumption that the IFR of COVID-19 derived from the Spanish data could be exported to other countries. Under these conditions the model could be used to explore the spread of COVID-19 in African and South American countries. Data on human mobility should also be available to permit studies of spatial spread, but since this is often not readily available in these contexts, with a bit of effort one could use spatially detailed tim...
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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