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BackgroundChikungunya fever (CHIKF) was first described in Tanzania in 1952. Several epidemics including East Africa have occurred, but there are no descriptions of longitudinal surveillance of endemic disease. Here, we estimate the incidence of CHIKF in coastal Kenya and describe the associated viral phylogeny.MethodsWe monitored acute febrile illnesses among 3500 children visiting two primary healthcare facilities in coastal Kenya over a 5-year period (2014-2018). Episodes were linked to a demographic surveillance system and blood samples obtained. Cross-sectional sampling in a community survey of a different group of 435 asymptomatic children in the same study location was done in 2016. Reverse-transcriptase PCR was used for chikungunya virus (CHIKV) screening, and viral genomes sequenced for phylogenetic analyses.ResultsWe 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 the community survey was 0.7% (95% CI 0.22, 2.12). CHIKF incidence among children ConclusionsCHIKF may be a substantial public health burden in primary healthcare on the East African coast outside epidemic years, and recurrent infections are common.

Original publication




Journal article


BMC infectious diseases

Publication Date





KEMRI-Wellcome Trust Research Programme, P.O. Box 230-80108, Kilifi, Kenya.


Humans, Chikungunya virus, Recurrence, Fever, Incidence, Prevalence, Prospective Studies, Cross-Sectional Studies, Phylogeny, Genotype, Adolescent, Child, Child, Preschool, Infant, Kenya, Female, Male, Chikungunya Fever