Introduction of dengue virus serotype 3 in the Afar Region, Ethiopia

Abstract

The genetic analysis of the Dengue virus circulating in Ethiopia's Afar region, in 2023, identified three distinct introductions with spatiotemporal clustering linked to genomes from Asia and Italy. These findings are crucial for enhancing prevention and control strategies, reinforcing the necessity to provide sustainable tools for genomic epidemiology in Africa.

Keywords: Ethiopia; Italy; dengue; genomic epidemiology; outbreak.

Figure 1.

Dynamics of DENV-3 in Ethiopia. (a) The percentage of DENV genome sequenced plotted against RT – qPCR Ct value for each sample (n = 7). Each circle represents a sequence recovered from an infected individual in Ethiopia and is coloured by sampling location; (b) Map of Ethiopia showing the sampling locations of new DENV-3 genome sequences by region and district. The size of the circles represents the number of new genomes generated in each district; (c) Time-stamped Maximum Likelihood tree including the novel DENV-3 sequences (n = 7) generated in this study, along with n = 351 reference strains belonging to DENV-3 genotype III sampled worldwide. Tips on the tree are annotated with circles and coloured based on their locations; (d) The inset tree on the right represent a Maximum Clade Credibility (MCC) tree, which estimates divergence times, inferred using a smaller dataset (n = 111) which included all novel genomes from Ethiopia. Each branch is coloured according to the legend on the left; Ethiopian sequences are marked with a black circle. Support for branching structure is shown by posterior probability values at key nodes; (e) Representation of the spatiotemporal reconstruction of the spread of DENV3-III Major lineage B.