Genomic monitoring and tracking of mpox virus clade Ib in Burundi between july to september 2024

Background: Since the first identification of mpox virus (MPXV) clade Ib in Burundi in July 2024, Burundi is one of the most affected countries in this evolving outbreak outside of the DRC. Methods: Here we aimed to understand the route(s) of introduction and spread of MPXV throughout the first months of the outbreak in Burundi. In total, 98 genome sequences from cases diagnosed during the first three months of the outbreak were generated. Results: Here we show using phylogenetic analysis that the virus was introduced from the DRC and Bayesian evolutionary analysis shows that different clusters could be identified in Burundi leading to further spread within the country. Conclusions: In summary, we identify sustained circulation of clade Ib MPXV in Burundi, most likely after several different introductions from the bordering province of South Kivu-DRC. The virus has acquired several additional APOBEC-3 mediated mutations, in line with reported evidence of ongoing human-to-human transmission.