Lineage B Genotype III of Dengue Virus Serotype 3 (DENV-3III_B) is responsible for Dengue Outbreak in Dire Dawa City, Ethiopia, 2023

Background: The eastern parts of Ethiopia, including Dire Dawa City, have faced annual dengue fever (DF) outbreaks since 2013, resulting in substantial healthcare and economic consequences. However, there remains a lack of comprehensive evidence regarding the specific dengue virus (DENV) serotypes and genotypes associated with those outbreaks. Methodology: On December 14, 2023, the National Arbovirus Laboratory at the Ethiopian Public Health Institute received seventy serum samples from 70 patients suspected of DF during the outbreak in Dire Dawa City. Samples positive for DENV with adequate volume and CT values underwent sequencing of the CprM region of the DENV genome. The obtained sequences were typed using the Dengue Virus Typing Tool and underwent phylogenetic analysis to evaluate sequence diversity and relationships to DENV strains from other global DENV-endemic regions. Results: Overall, 32 (45.7%) of the patients displayed one or more early warning signs indicative of severe dengue. Among the 13 patients who were hospitalized for 2 to 10 days, all except two had at least one symptom indicative of severe dengue. Out of 67 samples with adequate volume, 44 (65.6%) were positive for DENV RNA using RT-PCR, and 21 successfully underwent CprM sequencing. All of them belonged to DENV-3, genotype III, major lineage B (DENV-3III_B), but represented two different minor lineages (DENV-3III_B.2 and DENV-3III_B.3). Phylogenetic analysis demonstrated that both lineages were closely related to sequences from the Afar region of Ethiopia collected in 2023, indicating that the outbreaks were related and were due to multiple co-circulating lineages. Conclusions: DENV-3III_B was identified as the cause of the 2023 DF outbreak in Dire Dawa City. The identification of two co-circulating lineages in this outbreak underscores the complex nature of DENV transmission in the African continent and highlights the need for increased viral genomic surveillance.