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

Abstract

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.

Keywords: CprM; DENV; DENV-3/GIII; DF; Dire Dawa City; Ethiopia; genotype; serotype.

Figure 1

Map showing the Dire Dawa City Administration where the Dengue outbreak occurred, and the study of DENV strains originated. The shaded areas indicate the epicenters of dengue outbreaks in Ethiopia since 2013: Dire Dawa (red), Afar (red-violet), and Somalia (light blue).

Figure 2

Flow chart showing enrollment of suspected dengue and/or other febrile illnesses, including malaria patients, and molecular detection and characterization of strains isolated during the 2023 dengue outbreak in Dire Dawa, Ethiopia.

Figure 3

Maximum likelihood phylogenetic tree of DENV-3 genotype III (DENV-3III) strains isolated during the 2023 outbreak in Dire Dawa, Ethiopia. The tree includes CprM sequences newly generated in this study (red branches, N = 17) and representative reference sequences from DENV-3III (N = 942, sequences from Ethiopia in blue and other branches in black). The outer circles indicate continent of origin and the DENV-3III_B major and minor lineages. Nodes with ultrafast bootstrap values of 95 and above are indicated with black circles. The internal tree scale represents the number of nucleotide substitutions per site. A more detailed tree with branch labels, including accession number, country of origin, and year of isolation, as well as the percentages of support for the strains’ genotype, major lineage, and minor lineage assignments using recently developed DENV lineage assignment tools, can be found in Supplementary Figure S1 and Supplementary Table S1, respectively.