The World Health Organization recently declared the 2024 mpox virus (MPXV Ib) outbreak a public health emergency of international concern. We report that in 2023-2024, MPXV clade Ib genomes are diverging at a faster rate than clade IIb (2022), primarily due to an unusually high incidence of recombination. Phylogenetic analysis revealed that Ib strains have diverged into four lineages, and they have evolved into 14 subgroups based on nine tandem repeat (TR) polymorphisms. These findings confirms that TRs in MPXV Ib are mutating at a significantly higher frequency compared to the 2022 outbreak (clade IIb, 11 subgroups). Linkage disequilibrium analysis also identified 10 recombination clusters among all 4 lineages, with recombination incidence in Ib being twice as high as in IIb. This suggests that a higher rate of superinfection is contributing to ongoing recombination among populations infected with clade Ib. Prompt action is necessary to prevent the emergence of more lethal mpox strains.

The authors have declared no competing interest.

This study did not receive any funding

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