Real-time numerical forecast of global epidemic spreading: case study of 2009 A/H1N1pdm

Michele Tizzoni1, Paolo Bajardi1,2, Chiara Poletto1,3, José J Ramasco4, Duygu Balcan1, Bruno Gonçalves5, Nicola Perra5, Vittoria Colizza3,7,8 and Alessandro Vespignani6,8,9

1Computational Epidemiology Laboratory, Institute for Scientific Interchange (ISI), Torino, Italy.
2Department of Animal Production, Epidemiology and Ecology, Faculty of Veterinary Medicine, University of Torino, Italy.
3INSERM, U707, Paris, France.
4Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), Palma de Mallorca, Spain.
5Centre de Physique Théorique (CNRS UMR 6207), Marseille, France.
6Department of Health Sciences and College of Computer and Information Sciences, Northeastern University, Boston MA 02115 USA.
7UPMC Université Paris 06, Faculté de Médecine Pierre et Marie Curie, UMR S 707, Paris, France.
8Institute for Scientific Interchange (ISI), Torino, Italy.
9Institute for Quantitative Social Sciences at Harvard University, Cambridge MA, 02138 USA.

(Dec 2012)

Mathematical and computational models for infectious diseases are increasingly used to support public-health decisions; however, their reliability is currently under debate. Real-time forecasts of epidemic spread using data-driven models have been hindered by the technical challenges posed by parameter estimation and validation. Data gathered for the 2009 H1N1 influenza crisis represent an unprecedented opportunity to validate real-time model predictions and define the main success criteria for different approaches. We used the Global Epidemic and Mobility Model to generate stochastic simulations of epidemic spread worldwide, yielding (among other measures) the incidence and seeding events at a daily resolution for 3,362 subpopulations in 220 countries. Using a Monte Carlo Maximum Likelihood analysis, the model provided an estimate of the seasonal transmission potential through the Monte Carlo likelihood analysis and generated ensemble forecasts for the activity peaks in the northern hemisphere in the fall/winter wave. These results were validated against the real-life surveillance data collected in 48 countries, and their robustness assessed by focusing on 1) the peak timing of the pandemic; 2) the level of spatial resolution allowed by the model; and 3) the clinical attack rate and the effectiveness of the vaccine. In addition, we studied the effect of data incompleteness on the prediction reliability. Real-time predictions of the peak timing are found to be in good agreement with the empirical data, showing strong robustness to data that may not be accessible in real time (such as pre-exposure immunity and adherence to vaccination campaigns), but that affect the predictions for the attack rates. The timing and spatial unfolding of the pandemic are critically sensitive to the level of mobility data integrated into the model. Our results show that large-scale models can be used to provide valuable real-time forecasts of influenza spreading, but they require high-performance computing. The quality of the forecast depends on the level of data integration, thus stressing the need for high-quality data in population-based models, and of progressive updates of validated available empirical knowledge to inform these models.