Genomic Surveillance Unveils Mpox Clade IIb Spread in Kinshasa

Public health investigators identified mpox Clade IIb introduced into Kinshasa; genomic assignment determined the responsible lineage as lineage G.1. Clinical presentation and immediate contact investigation signaled onward spread among close contacts, consistent with an importation followed by local transmission.

Tiled-amplicon whole-genome sequencing of specimens collected from the index patient and close contacts in July 2025 confirmed the introduction. Four consensus genomes—from paired vesicle and blood or nasopharyngeal samples with 80–94% horizontal coverage—clustered tightly within Clade IIb/sh2017 and aligned to Sierra Leone sequences sampled earlier in 2025. The laboratory workflow used Clade IIb–specific primer pools, triplicate library preparations, and long-read sequencing; phylogenetic placement was consistent across specimen types, supporting importation with local spread.

Sequencing linked the index case to secondary infections within a household and immediate-contact network. Near-identical genomes among the four samples, together with short symptom-onset intervals (index sampled mid‑July 2025; secondary sampled within two days of last exposure), provide direct evidence of transmission. Epidemiologic tracing tied exposures to household and partner contact; there was no reported zoonotic exposure in the index case’s recent travel history. Phylogenetic topology shows a single, tightly clustered Kinshasa clade that nests with Sierra Leone sequences rather than multiple discrete Kinshasa lineages, and APOBEC3-type substitutions differentiate the cluster by only a small number of SNPs—consistent with sustained human-to-human transmission following a single introduction.

These genomic and epidemiologic observations change operational priorities for the Kinshasa response. Targeted case-finding in households and immediate social networks, prioritized sequencing of suspected Clade IIb specimens, and focused cross-border contact investigation will better define transmission corridors without implying broader population-level prevalence. Rapid laboratory confirmation enables phylogenetic linkage; maintaining sequencing capacity and expediting sample flow from isolation units permit near–real-time mapping of chains. Strengthening laboratory-to-field workflows will improve resolution of transmission links while routine surveillance continues.