Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022-2023

Abstract

In Ethiopia, dengue virus (DENV) infections have been reported in several regions; however, little is known about the genetic diversity of circulating viruses. We conducted clinical surveillance of DENV during the 2023 nationwide outbreak in Ethiopia. We enrolled patients at 3 sentinel hospital sites. Using reverse transcription PCR, we screened serum samples for 3 arboviruses and then serotyped and whole-genome sequenced DENV-positive samples. We detected DENV-1 and DENV-3 serotypes. Phylogenetic analysis identified 1 transmission cluster for DENV-1 (genotype III major lineage A) and 2 clusters for DENV-3 (genotype III major lineage B). The first DENV-3 cluster was closely related to an isolate from a 2023 dengue outbreak in Italy; the second cluster was related to isolates from India. Co-circulation of DENV-1 and DENV-3 in Ethiopia highlights the potential for severe dengue. Intensified surveillance and coordinated public health responses are needed to address the threat of severe dengue outbreaks.

Keywords: DENV; Ethiopia; dengue; dengue virus; genotype; human mobility; phylogenetic analysis; seasonality; serotype; vector-borne infections; viruses; zoonoses.

Figure 1

Spatiotemporal distribution of dengue cases in study of genomic characterization of circulating DENV, Ethiopia, 2022–2023. A–C) Number of dengue cases in Ethiopia in Afar Region during April 2023–August 2023 outbreak (A), Dire Dawa during June 2023–April 2024 outbreak (B), and national count during 2023–2024 (C). Each colored vertical line under bars indicates 1 sequenced genome. D) DENV serotype distribution of sampled cases. Size of circles indicates number of genotyped cases for each serotype. DENV, dengue virus.

Figure 2

Number of dengue cases in different regions of Ethiopia during 2023–2024 in study of genomic characterization of circulating dengue virus. Only dengue virus (DENV) serotype 3 was found in Afar Region; both DENV-1 and DENV-3 were isolated in the city of Dire Dawa.

Figure 3

Demographic distribution of patients with dengue virus infections in study of genomic characterization of circulating dengue virus, Ethiopia, 2022–2023.

Figure 4

Sequencing process and coverage results in study of genomic characterization of circulating DENV, Ethiopia, 2022–2023. A) Patient sample selection, genotyping, and sequencing workflow. B) PCR cycle thresholds compared with sequence coverage for all sequenced specimens from Afar Regions and Dire Dawa. DENV, dengue virus; III-A, genotype III lineage A; III-B, genotype III lineage B; RT-PCR, reverse transcription PCR.

Figure 5

Time-scaled phylogenetic analysis of genomes from Ethiopia in study of genomic characterization of circulating dengue virus (DENV), 2022–2023. A) Time-scaled maximum-likelihood phylogeny of DENV-1 genotype III major lineage A clade sequences containing sequenced genomes from this study. B) Time-scaled phylogeny of subclade of tree in panel A, indicating close evolutionary relationships of DENV-1 sequences from Ethiopia. C) Time-scaled maximum-likelihood phylogeny of DENV-3 genotype III major lineage B clade sequences containing sequenced genomes from this study. D) Time-scaled maximum clade credibility tree of subclade from tree in panel C indicating phylogenetic relationships of cluster 1 of DENV-3 genomes from Ethiopia. E) Time-scaled maximum clade credibility tree of subclade from tree in panel C indicating phylogenetic relationships of cluster 2 of DENV-3 genomes from Ethiopia. Colors indicate country or continent origin of sequences used in trees.