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During the 2004–2005 influenza season two independent influenza surveillance systems operated simultaneously in three United States counties. The New Vaccine Surveillance Network (NVSN) prospectively enrolled children hospitalized for respiratory symptoms/fever and tested them using culture and RT–PCR. The Emerging Infections Program (EIP) and a similar clinical-laboratory surveillance system identified hospitalized children who had positive influenza tests obtained as part of their usual medical care. Using data from these systems, we applied capture–recapture analyses to estimate the burden of influenza related-hospitalizations in children aged <5 years. During the 2004–2005 influenza season the influenza-related hospitalization rate estimated by capture–recapture analysis was 8·6/10 000 children aged <5 years. When compared to this estimate, the sensitivity of the prospective surveillance system was 69% and the sensitivity of the clinical-laboratory based system was 39%. In the face of limited resources and an increasing need for influenza surveillance, capture–recapture analysis provides better estimates than either system alone.
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