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The relationship of enterovirus (EV) infection and Kawasaki disease (KD) is still unclear. The purpose of this study was to conduct a population-based cohort study to determine the relationship between KD and EV infection in Taiwan.A population-based cohort study was conducted to analyze the children file (age < 18 years) of the Taiwan National Health Insurance program between 2000 and 2008. In total, 285,636 children with EV infection and 285,636 children without EV infection were included and followed up. The subsequent KD was the major outcome event.The cumulative incidence of KD was significantly higher in the EV-infected cohort than in the non-EV–infected cohort (log-rank test, P < 0.001). The overall incidence of KD was 56% higher in the EV-infected cohort than in the non-EV–infected cohort, with an adjusted hazard ratio of 1.56 (95% confidence interval: 1.44–1.69). Stratified analysis showed higher KD risk associated with previous EV infection in children 3–5 years old, in girls, in children living in less urbanization levels, in children with parental low-income occupation, and in children with allergic diseases.There is a higher association between KD and previous EV infection in Taiwanese children, especially in those 3–5 years old, with female sex, with less urbanization level, with low-income parental occupation, and with allergy.