Molecular characterization of chikungunya viruses associated with outbreaks in Kenya from 2017 to 2020

Emerging outbreaks of the arbovirus chikungunya virus affect millions of individuals globally, causing debilitating arthralgia and fever. A study on the burden and etiologies of acute febrile illnesses (AFI) in Kenya reported an increase in CHIKV cases in Mombasa between December 2017 and December 2019. In January and February 2020, another outbreak of CHIKV occurred in Dadaab-Hagadera. Using next-generation sequencing on the Illumina MiSeq platform, we established molecular characteristics and phylogenetic differences of the CHIKVs collected from the two epidemiologically distinct settings. Sequenced viruses belonged to the Indian Ocean Lineage and clustered according to geographic region, with E1:K211E and E2:V264A mutations present in both settings. Additional mutations previously reported during Kenyan CHIKV outbreaks and suggested to influence CHIKV adaptation to Aedes albopictus, including E1:T82I and E1:V84D, were also identified. These molecular markers provide useful information on CHIKV spread and can help strengthen outbreak preparedness and response. Clinical features were described only for laboratory-confirmed CHIKV cases from the AFI surveillance cohort and compared with AFI cases testing negative for CHIKV. Sore muscles, headache, and convulsions were more frequently reported among CHIKV-positive participants, whereas diarrhea was less common. No differences were observed in the frequency of cough, skin rash, conjunctivitis, or vomiting. Given the limited number of confirmed CHIKV cases and the predominance of young children in the cohort, the reported clinical symptom associations should only be interpreted as exploratory and warrant confirmation in larger and more representative populations.