Endemic Chikungunya Fever in Kenyan Children

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 ≥ 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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was commissioned by the National Institute for Health Research (NIHR) Global Health Research programme [16/136/33] using UK aid from the UK Government. The views expressed in this publication are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. GMW is supported by an Oak foundation fellowship and a Wellcome Trust grant [grant number 203077\_Z\_16_Z]. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was provided by the Kenya Medical Research Institute Scientific and Ethics Review Unit All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The replication data and analysis scripts for this manuscript shall be made available at the Harvard Dataverse: (https://dataverse.harvard.edu/dataverse/kwtrp). Some of the clinical dataset contains potentially identifying information on participants and is stored under restricted access. Requests for access to the restricted dataset should be made to the Data Governance Committee (dgc@kemri-wellcome.org) of the KEMRI-Wellcome Trust Research Programme.