Chikungunya virus (CHIKV) has originated from Africa and has spread worldwide. Since 2017, multiple chikungunya outbreaks were reported in the Horn of Africa, without molecular characterization. In November 2019, an autochthonous acute chikungunya infection was diagnosed in a French patient living in Djibouti, marking the reemergence of the virus in the country. The strain was isolated and fully sequenced. Phylogenetic analysis revealed the Djiboutian strain belongs to the Indian lineage of the ECSA genotype. Two mutations highly increasing the virus' fitness in Aedes aegypti, the sole vector present in Djibouti city, were identified.
Keywords: Chikungunya virus; Djibouti; Horn of Africa; sequencing; traveler.
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