1
|
Sherratt K, Srivastava A, Ainslie K, Singh DE, Cublier A, Marinescu MC, Carretero J, Garcia AC, Franco N, Willem L, Abrams S, Faes C, Beutels P, Hens N, Müller S, Charlton B, Ewert R, Paltra S, Rakow C, Rehmann J, Conrad T, Schütte C, Nagel K, Abbott S, Grah R, Niehus R, Prasse B, Sandmann F, Funk S. Characterising information gains and losses when collecting multiple epidemic model outputs. Epidemics 2024; 47:100765. [PMID: 38643546 DOI: 10.1016/j.epidem.2024.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results. METHODS We compared projections from the European COVID-19 Scenario Modelling Hub. Five teams modelled incidence in Belgium, the Netherlands, and Spain. We compared July 2022 projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model's quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data. RESULTS By collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models' quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes. CONCLUSIONS We observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort's aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts.
Collapse
Affiliation(s)
| | | | - Kylie Ainslie
- Dutch National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands; School of Public Health, University of Hong Kong, Hong Kong Special Administrative Region
| | | | | | | | | | | | | | | | - Steven Abrams
- University of Antwerp, Antwerp, Belgium; UHasselt, Hasselt, Belgium
| | | | | | - Niel Hens
- University of Antwerp, Antwerp, Belgium; UHasselt, Hasselt, Belgium
| | | | | | | | | | | | | | - Tim Conrad
- Zuse Institute Berlin (ZIB), Berlin, Germany
| | | | - Kai Nagel
- Technische Universität Berlin, Berlin, Germany
| | - Sam Abbott
- London School of Hygiene & Tropical Medicine, London, UK
| | | | | | | | | | - Sebastian Funk
- London School of Hygiene & Tropical Medicine, London, UK
| |
Collapse
|
2
|
Müller SA, Balmer M, Charlton W, Ewert R, Neumann A, Rakow C, Schlenther T, Nagel K. Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data. PLoS One 2021; 16:e0259037. [PMID: 34710158 PMCID: PMC8553173 DOI: 10.1371/journal.pone.0259037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022] Open
Abstract
Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines a well-established approach from transportation modelling that uses person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. The model includes the consequences of different room sizes, air exchange rates, disease import, changed activity participation rates over time (coming from mobility data), masks, indoors vs. outdoors leisure activities, and of contact tracing. It is validated against the infection dynamics in Berlin (Germany). The model can be used to understand the contributions of different activity types to the infection dynamics over time. It predicts the effects of contact reductions, school closures/vacations, masks, or the effect of moving leisure activities from outdoors to indoors in fall, and is thus able to quantitatively predict the consequences of interventions. It is shown that these effects are best given as additive changes of the reproduction number R. The model also explains why contact reductions have decreasing marginal returns, i.e. the first 50% of contact reductions have considerably more effect than the second 50%. Our work shows that is is possible to build detailed epidemiological simulations from microscopic mobility models relatively quickly. They can be used to investigate mechanical aspects of the dynamics, such as the transmission from political decisions via human behavior to infections, consequences of different lockdown measures, or consequences of wearing masks in certain situations. The results can be used to inform political decisions.
Collapse
Affiliation(s)
- Sebastian A. Müller
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | | | - William Charlton
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Ricardo Ewert
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | | | - Christian Rakow
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Tilmann Schlenther
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Kai Nagel
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| |
Collapse
|
3
|
Müller SA, Balmer M, Charlton W, Ewert R, Neumann A, Rakow C, Schlenther T, Nagel K. Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data. PLoS One 2021; 16:e0259037. [PMID: 34710158 DOI: 10.1101/2021.02.27.21252583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/12/2021] [Indexed: 05/24/2023] Open
Abstract
Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines a well-established approach from transportation modelling that uses person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. The model includes the consequences of different room sizes, air exchange rates, disease import, changed activity participation rates over time (coming from mobility data), masks, indoors vs. outdoors leisure activities, and of contact tracing. It is validated against the infection dynamics in Berlin (Germany). The model can be used to understand the contributions of different activity types to the infection dynamics over time. It predicts the effects of contact reductions, school closures/vacations, masks, or the effect of moving leisure activities from outdoors to indoors in fall, and is thus able to quantitatively predict the consequences of interventions. It is shown that these effects are best given as additive changes of the reproduction number R. The model also explains why contact reductions have decreasing marginal returns, i.e. the first 50% of contact reductions have considerably more effect than the second 50%. Our work shows that is is possible to build detailed epidemiological simulations from microscopic mobility models relatively quickly. They can be used to investigate mechanical aspects of the dynamics, such as the transmission from political decisions via human behavior to infections, consequences of different lockdown measures, or consequences of wearing masks in certain situations. The results can be used to inform political decisions.
Collapse
Affiliation(s)
- Sebastian A Müller
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | | | - William Charlton
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Ricardo Ewert
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | | | - Christian Rakow
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Tilmann Schlenther
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| | - Kai Nagel
- Transport Systems Planning and Transport Telematics, TU Berlin, Berlin, Germany
| |
Collapse
|