Genomic epidemiology of the 2025 mpox epidemic in Sierra Leone
Summary
Mpox is a re-emerging zoonotic disease caused by MPXV, which has led to outbreaks across multiple countries in recent years. Sierra Leone reported its first mpox case in 8 years in January 2025, rapidly becoming the epicenter of a continental outbreak with more than 5,000 confirmed cases by August, a surge with unknown origins, timings and drivers. Phylodynamic analyses using 338 genomes generated from 14 districts suggests that the outbreak was caused by lineage G.1 (A.2.2.1) which descen
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# Genomic epidemiology of the 2025 mpox epidemic in Sierra Leone
*Published: 2026 May*
Mpox is a re-emerging zoonotic disease caused by MPXV, which has led to
outbreaks across multiple countries in recent years. Sierra Leone reported its
first mpox case in 8 years in January 2025, rapidly becoming the epicenter of a
continental outbreak with more than 5,000 confirmed cases by August, a surge
with unknown origins, timings and drivers. Phylodynamic analyses using 338
genomes generated from 14 districts suggests that the outbreak was caused by
lineage G.1 (A.2.2.1) which descended from lineages circulating in Nigeria. Here
we observed a strong APOBEC3 mutational enrichment, consistent with sustained
human transmission that circulated undetected for ~3 months before the first
confirmed case in January 2025. The Western Area Urban district served as the
primary hub for nationwide spread and persistence, as well as multiple
international export events. We further estimated that the true epidemic size
was nearly double official case counts, highlighting substantial surveillance
gaps. These findings underscore the urgent need for strengthened genomic and
diagnostic surveillance systems across West Africa to pre-empt epidemics.
DOI: 10.1038/s41591-026-04385-8