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

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. 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. 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. 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. Mpox is a viral infection caused by the mpox virus (MPXV). A specific MPXV strain called lb, is spreading in the Eastern African region. Here, we aimed to understand how this strain was introduced into Burundi and spread to the rest of the country using genetic sequencing. Using this data, we could track the genetic evolution of the virus and found that there were several different introductions of the virus into Burundi, or that the virus had already been circulating in the country since around May 2024. Additionally, we identified specific mutations in the virus, indicative of human-to-human transmission (APOBEC-3). These findings suggest there is sustained circulation of mpox MPXV Ib in Burundi, largely driven by human-to-human transmission. Nzoyikorera et al. describe the genomic surveillance efforts following introduction of the mpox clade Ib virus into Burundi. They demonstrate sustained circulation of clade Ib in Burundi and discuss the potential routes of introduction from neighbouring regions.