Emergence of human monkeypox virus Clade Ib in Madagascar: first genomic evidence of introduction and local transmission.

In December 2025, Madagascar reported its first confirmed cases of mpox, coinciding with the regional expansion of human monkeypox virus (MPV) Clade Ib across Central and East Africa. To characterize this outbreak, we generated the first near-complete MPV genome sequences from Madagascar using an amplicon-based nanopore sequencing approach applied directly to clinical samples. Eleven high-quality genomes were analyzed using maximum likelihood phylogenetics and Nextclade lineage assignment. All Malagasy sequences clustered within MPV Clade Ib and were closely related to strains circulating in the Democratic Republic of the Congo and Uganda during 2024-2025. Phylogenetic reconstruction supports a recent introduction from mainland Africa, followed by local transmission. The genetic homogeneity observed among Malagasy sequences supports a limited number of introduction events during the early phase of the outbreak. These findings provide the first genomic evidence of Clade Ib circulation in Madagascar. Our study underscores the value of rapid genomic surveillance in island settings to detect viral introductions, inform public health responses, and anticipate further dissemination across islands of the south-west Indian Ocean.