Case Study: 2009 H1N1 Pandemic

Case Study: 2009 H1N1 Pandemic

US early outbreak: real vs. simulated geographic pattern

The coupled animations show the geotemporal evolution of the swine flu epidemic in the United States, by comparing the observed pattern (left) with the simulated one (right). Simulations refer to the baseline scenario obtained from the maximum likelihood analysis used to estimate the transmission potential of the new influenza A(H1N1) (see this post for more details) [1]. Simulations are not iteratively calibrated, and containment or mitigation interventions are not considered in the model. The maps represent the geographic distribution of the cumulative number of cases at a resolution level of ¼°. Both maps adopt the same color code ranging from a minimum of 1 case per cell (pink) to the maximum number of cases per cell reached in the time frame explored (red). This allows a one-to-one comparison of the two epidemics at each date, highlighting analogies and differences of the geographic spread and of the epidemic activity in terms of number of cases. The data reported on the ‘Real map’ is obtained from official sources and projected at this level of resolution, accessible by the model in the simulations. The data reported on the ‘Simulated map’ is obtained from the average value calculated on 2,000 stochastic realizations of the model. The timeline shown is from May 1, 2009 to July 6, 2009, after which date it was no longer possible to track confirmed cases at this level of resolution.

The comparison shows that the simulations produce an epidemic spread in good agreement with the outbreak observed in reality, being able to identify the major hot zones during the early stage of the outbreak and to correctly predict the time evolution of the propagation. However differences are observed, as e.g. the large epidemic activity predicted in Atlanta that does not correspond to the reported cases, or the presence of small outbreaks in some regions of the country that are not reproduced by the model. Mismatches in areas with a very small number of cases (light pink) can be due to fluctuations that the model is not able to reproduce. They correspond indeed to very small outbreaks of 1 to 10 cases, which are more prone to noise, especially during the early phase of the outbreak. In largely populated areas where an outbreak occurred, our simulations result in a larger epidemic than what was reported by official sources. This difference is induced by the surveillance and monitoring systems that are not able to track all ill individuals in the country and confirm their infection by H1N1 by serological tests. The simulation results mapped here below do not take into account a probability of detection, and therefore the color quantifies the total number of cases predicted by the model. A comparison between the real cases and the simulated cases can be used to provide a quantitative estimation of the detection rate of the monitoring systems.

[1] Balcan D et al, Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility. BMC Medicine 2009, 7:45.



Real cases map.
Simulated cases map.
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