Predominance of Dengue Virus Serotype-1/Genotype-I in Eastern and Southeastern Ethiopia

Abstract

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.

Keywords: Ethiopia; capsid/pre-membrane (CprM); dengue virus; genotype; outbreak; phylogenetic analysis; sequence; serotype.

Figure 1

Map of Ethiopia showing districts affected by dengue during in the 2014–2016 and 2021 outbreaks, and from which DENV strains were sequenced.

Figure 2

Genotyping of DENV-1 strains using the Dengue Virus Typing Tool. Blue circles represent the strains from this study, while others are reference strains, represented with their GenBank accession numbers and numbers representing the serotype and genotypes included in the analysis.

Figure 3

Genotyping of DENV-2 strains using the Dengue Virus Typing Tool. Blue circles represent the strains from this study, while others are reference strains, represented with their GenBank accession numbers and numbers representing the serotype and genotypes included in the analysis.

Figure 4

Phylogenetic analysis of DENV-1 sequences from outbreaks in Eastern and Southeastern Ethiopia. Evolutionary history was inferred by using the maximum-likelihood phylogenies. (A) Phylogenetic tree topology of DENV-1 sequences (N = 2442), classified by genotypes. The Genotype-I and Genotype-III sequences from this study are shown in red and blue branches, respectively. (B) Phylogenetic tree of the selected DENV-1 Genotype-I sequences is indicated by the blue rectangle in the light-green-shaded section of the panel (A). The sequences from this study are shown in red. (C) Phylogenetic tree of the selected DENV-1 Genotype-III sequences is indicated by the red rectangle in the light-pink-shaded section of the panel (A). The sequences from this study are shown in blue. Panel (B,C): sequences in the trees are shown by their country of origin and year of sample collection. The scale bar indicates the genetic distance. Only bootstrap values greater than 70% are shown in the phylogenic trees.

Figure 5

Phylogenetic analysis of DENV-2 sequences from outbreaks in Eastern and Southeastern Ethiopia. Evolutionary history was inferred by using the maximum-likelihood phylogenies. (A) Phylogenetic tree topology of DENV-2 serotype sequences (N = 1911), classified by genotypes. The sequences from this study are shown in green branches. (B) The phylogenetic tree of the selected DENV-2, Cosmopolitan Genotype sequences is indicated by the red rectangle in the light-pink-shaded section of the panel (A). Sequences in the tree are shown by their country of origin and year of sample collection. The sequences from this study are shown in green. The scale bar indicates the genetic distance. Only bootstrap values greater than 70% are shown in the phylogenic trees.