The eastern parts of Ethiopia, including Dire Dawa City, have experienced annual dengue fever (DF) outbreaks since 2013, leading to significant healthcare and economic impacts. However, comprehensive evidence on the specific dengue virus (DENV) serotypes and genotypes involved remains limited. During the 2023 DF outbreak, the National Arbovirus Laboratory received seventy serum samples from suspected DF patients. Positive samples underwent sequencing of the CprM region of the DENV genome, and the obtained sequences were analyzed phylogenetically. Among the patients, 32 (45.7%) displayed early warning signs of severe dengue, and 13 were hospitalized, most showing symptoms indicative of severe dengue. Out of 67 adequate samples, 44 (65.6%) tested positive for DENV RNA by RT-PCR, and 17 successfully underwent CprM sequencing. All sequenced samples were identified as DENV-3, genotype III, major lineage B (DENV-3III_B), with two distinct minor lineages (DENV-3III_B.2 and DENV-3III_B.3). Phylogenetic analysis showed that these lineages were closely related to sequences from the Afar region, suggesting interconnected outbreaks with multiple co-circulating lineages. This study identifies DENV-3III_B as the cause of the 2023 DF outbreak in Dire Dawa City and highlights the need for enhanced viral genomic surveillance in Africa.

We determined the dengue virus (DENV) serotypes and genotypes in archived serum samples that were collected during the 2014–2016 and 2021 dengue outbreaks in Dire Dawa City and the Somali region in Ethiopia. DENV serotype 1 (DENV-1) was predominant followed by DENV serotype 2 (DENV-2). Thirteen of the DENV-1 strains were assigned to Genotype-I, while the remaining two were found to be Genotype-III. All three DENV-2 strains were assigned the Cosmopolitan Genotype. The DENV strains responsible for the outbreaks are genetically closely related to the DENV strains that circulated in neighboring and Asian countries. The findings also showed continued local transmission of a monophyletic lineage and a co-circulation of DENV-1 and DENV-2 during the outbreaks. There is a need to strengthen DENV genomic surveillance capacity for the early detection of circulating serotypes, and prevent devastating consequences of future outbreaks due to the co-circulation of different serotypes.