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Background. Chikungunya virus (CHIKV) was first identified in Tanzania in 1952. Several epidemics including East Africa are described, but there are no descriptions of longitudinal surveillance of endemic disease. Here, we estimate the incidence of CHIKV and describe viral phylogeny in coastal Kenya. Methods. Over a 5-year period (2014-2018), 11,708 febrile illnesses in 5,569 children visiting two primary healthcare facilities linked to a demographic surveillance system in coastal Kenya were recorded and blood samples obtained. Reverse-transcriptase PCR was used to identify CHIKF cases in 3,500 children randomly selected from the 5,569 children. Results. We found CHIKF to be endemic in this setting, associated with 12.7% (95% CI 11.60, 13.80) of all febrile presentations to primary healthcare. The prevalence of CHIKV infections among asymptomatic children in a community survey was 0.7% (95% CI 0.22, 2.12). CHIKF incidence among children <1 year of age was 1703 cases/100,000-person years and 46 cases/100,000-person years among children aged [&ge;] 10 years. Recurrent CHIKF episodes, associated with fever and viraemia, were observed among 19 of 170 children with multiple febrile episodes during the study period and confirmed by genome sequencing. All sequenced viral genomes mapped to the ECSA genotype albeit distinct from CHIKV strains associated with the 2004 East African epidemic. Conclusions. CHIKF may be a substantial public health burden in primary healthcare on the East African coast outside epidemic years, and recurrent infections are common.

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