Genomic characterization of dengue circulation in Togo, 2024

Togo experienced its first nationally reported dengue outbreak in 2024 amid a broader resurgence of dengue across Africa. Data on serotype distribution, genomic diversity, and transmission dynamics in the region were limited. Here, we integrated epidemiological, genomic, and environmental analyses to characterize the origins and spread of dengue transmission in Togo. Of 475 samples tested, 213 (44.8%) were dengue virus (DENV) positive by PCR. Of these, 190 samples (Ct < 35) were serotyped and 159 of those successfully serotyped underwent whole-genome sequencing. Sequencing generated one DENV-3 genome and 129 DENV-1 genomes, predominantly of genotype III lineage A.2. Our phylogenetic results suggest importation of this lineage from Tanzania into West Africa and Togo, linked to a large Tanzanian outbreak in 2019. Time-scaled phylogenies indicated the timing of introduction likely goes back early 2020, with cryptic circulation preceding the detected outbreak. Bayesian phylogeographic reconstruction support the inference of one common introduction into Togo/West-Africa and identified short- and long-range viral movements nationally and regionally. We conclude that 2024 dengue epidemic in Togo resulted from a single introduction followed by extensive local and regional spread facilitated by favourable environmental conditions and human mobility. In addition, this study doubles the number of available West African DENV-1-III A.2 genomes and highlights significant gaps in regional genomic surveillance that present challenges in understanding transmission pathways. Integrated, high-resolution genomic and epidemiological monitoring for dengue is essential for national and regional preparedness, readiness and response.