Refined Diagnostic Implementation Simulator for COVID-19 now online
© 2021 EPFL
Living with the effects of the SARS-CoV-2 virus (COVID-19) for nearly two years, we have all come to understand the importance and role of diagnostic testing in responding effectively to the immense threat of COVID-19. Back in early 2020, the EPFL Blue Brain Project and FIND, the global alliance for diagnostics, collaborated to develop a Diagnostic Implementation Simulator for SARS-CoV-2 diagnostics, which uses modelling data to simulate scenarios and estimate the potential impact of deploying different testing strategies for COVID-19. The collaboration has today released an updated version of the Simulator, which has evolved to keep pace with the specific needs of COVID-19 and address public health requirements. The Simulator is now capable of modelling specific testing scenarios and multiple pandemic phases.
Expert modeler, Richard Walker, working in close collaboration with his Blue Brain colleagues, FIND (who co-convene the Access to COVID-19 Tools [ACT] Accelerator Diagnostics Pillar), and a team from Ateneo de Manila University, Manila, the Philippines, built the Diagnostic Implementation Simulator based on the well-accepted SIR (susceptible/exposed, infected and recovered) theoretical model of epidemics. “Initially the modelling data ranked the potential impacts of deploying different testing strategies for COVID-19 on key outcomes in the early phase of the pandemic,” explains Richard. “As the global health crisis has persisted over several waves, we continued collaborating to keep developing the Simulator as more data became available, more knowledge was shared and advances in the types and efficacy of testing emerged. This has resulted in a new version, which now accommodates more phases (as many as required) and simulates a bigger range of options.”
As part of the simple three-step process, the user is first able to see the current state of the pandemic in their chosen country (information for 181 countries is available) and the current state of testing. Next, they can define intervention scenarios through four options: 1) no testing, 2) high contact groups first, 3) symptomatic first, 4) open public testing, within the scope of the current phase and any additional phases they wish to simulate. These also take into account parameters such as government intervention, contact testing and types of tests.
The primary role of the Simulator is to enable potential scenarios to be explored. These can range from simulating the results of moving to mass testing from a policy of only testing those with symptoms; simulating the results of no testing or intervention, or simulating the potential results of different types of tests.
“Testing rates remain highly variable across the world, reflecting significant ongoing inequality in access to tests,” said Stefano Ongarello, Head of Data Science at FIND. “This update to the Diagnostic Implementation Simulator refines the original model by adding more parameters to mimic more closely the potential high-level impact of different testing strategies, and their interaction with social strategies.”
Importantly, while the parameters are currently COVID-19 specific, the work devoted to the tool in the past eighteen months means it can be used for different viruses or crises in the future by adjusting the parameters accordingly, thereby providing a tool that can be quickly deployed for future public health emergencies.
Prof. Henry Markram, Founder and Director of the Blue Brain summarizes, “I am extremely proud of the dedication from the Blue Brain team of Software engineers, UX/UI design, Project Management and Communications. They have effortlessly pivoted the Blue Brain’s team science approach from our day-to-day work of digitally reconstructing and simulating the mouse brain, to first creating and then further refining the Diagnostic Implementation Simulator. Furthermore, as per our open science policy, we have open sourced the Simulator. Now anyone can look into how it works, contribute to it, or suggest improvements as time and circumstances evolve”.
To access the Diagnostic Implementation Simulator, click here - www.finddx.org/covid-19/dx-imp-sim
About the Diagnostic Implementation Simulator - www.finddx.org/covid-19/dx-imp-sim/about
Open Source repository - https://github.com/BlueBrain/covid-19-find
Contact us
Questions on using the Simulator – FIND - [email protected]
Questions about the modelling – Richard Walker
Notes
The resources needed to populate the Simulator are readily available and anyone can benefit from this easy-to-use tool, which works on both mobile and desktop.
This tool is not intended to replace detailed epidemiological models for country decision making or the estimates of deaths and of epidemic duration coming from such models.
It should also be noted that as is the case for any simulator/model, it relies on publicly reported information, which has not been independently verified.