Genomic investigation reveals local persistence and regional circulation of dengue virus associated with recent outbreaks in Kenya

Dengue is an arbovirus disease caused by dengue virus. The virus has recently caused a global surge in cases, with Africa reporting over 250 million and 900 deaths since 2023. This study was conducted during the 2023 dengue outbreak in Mombasa, with the aim of understanding outbreak cases in the context of earlier cases and recent global epidemics. During the 2023 outbreak, 56 of 406 samples tested positive for DENV: including DENV-1, DENV-2, and DENV-3. The study generated 38 whole genome sequences, 24 from 2023 to 14 from cases identified between 2020 and 2025. Phylogenetic analysis showed DENV-2 exhibited patterns suggesting long-term local circulation, while DENV-1 and DENV-3 were more widespread regionally, and are linked to recent outbreaks in Eastern and Western Africa. These findings highlight the need for integrated strategies to curb dengue in Kenya, such as measures to disrupt local transmission as well as importation of new strains.