Little is known about how best to deploy scarce resources for disease control when epidemics occur in different but interconnected regions. We use a combination of optimal control methods and epidemiological theory for metapopulations to address this problem. We consider what strategy should be used if the objective is to minimize the discounted number of infected individuals during the course of an epidemic. We show, for a system with two interconnected regions and an epidemic in which infected individuals recover and can be reinfected, that equalizing infection in the two regions is the worst possible strategy in minimizing the total level of infection. Treatment should instead be preferentially directed at the region with the lower level of infection, treating the other subpopulation only when there is resource left over. The same strategy holds with preferential treatments of regions with lower levels of infection when quarantine is introduced.
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