Genomic characterization of the 2024/2025 Mpox outbreak in Uganda

Abstract

Mpox has historically been endemic in Central and West Africa, driven by recurrent zoonotic spillover events, but recent outbreaks in East Africa underscore its expanding geographic footprint. Despite this shift, genomic data from East Africa remain limited. We performed genomic characterization of the 2024/2025 Mpox outbreak in Uganda using PCR-confirmed monkeypox virus (MPXV) positive samples (n=511) from 44 districts, all achieving ≥70% genome coverage. To provide regional context, we incorporated 895 publicly available clade Ib MPXV genomes from GISAID, Pathoplexus, and NCBI. Phylogenetic analysis revealed two major clusters within clade Ib, each subdivided into two subclusters, indicating substantial viral diversification. Most Ugandan sequences clustered within the most genetically diverse subcluster. Additional Ugandan genomes were distributed across other subclusters, indicating co-circulation of multiple lineages. Cluster 1 was dominated by sequences from the Democratic Republic of Congo, while phylogeographic analysis identified multiple cross-border introductions into Uganda. These findings highlight the role of regional connectivity in shaping MPXV transmission and underscore the importance of integrated genomic surveillance and cross-border data sharing to inform outbreak response in East and Central Africa.