# Genomic Characterization of the Index Case of Human Monkeypox Virus Infection in Mali, 2025

## TL;DR

This paper reports the genomic analysis of the first human monkeypox case in Mali, revealing mutations and linking it to an outbreak in Sierra Leone.

## Contribution

The study provides the first genomic characterization of the index monkeypox case in Mali and links it to a specific outbreak lineage.

## Key findings

- The Mali index case genome belongs to the Clade IIb G1 lineage with 85 mutations compared to a reference genome.
- Phylogeographic analysis links the Mali case to the May 2025 Sierra Leone outbreak.
- Genomic data was compared with other sequences to understand the epidemiological context.

## Abstract

Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali’s index Mpox case, which was clinically identified at the Mali–Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR™ MPXV Sequencing Library Prep and sequenced on Minion MK1C revealed a genome length of 197,122 bp with an average depth of 1284.4×. The strain belonged to Clade IIb G1 lineage and exhibited 85 mutations relative to NC_063383.1. To decipher genomic epidemiology, genomes ≥ 195 kb were retrieved from NCBI and aligned with MAFFT. Time-resolved phylogenetic reconstruction and ancestral trait inference were performed with TreeTime v0.11.4. A median joining network was built with Popart v1.7. Phylogeographic analysis revealed clustering with Clade IIb (G.1 lineage) linked to the May 2025 outbreak in Sierra Leone.