Phylodynamic inference suggests introductions as main driver of Mpox Clade II outbreak in 2022 in Slovenia.

In 2022, an Mpox clade II outbreak affected many countries. To optimize control, knowledge on the number of new introductions (human cases infected from outside the study population) versus local transmission is important. We extracted sequences of all 48 Mpox cases in Slovenia in 2022 from the NCBI database, of which 42 passed quality control. We estimated the number of introductions using the phylodynamic model phybreak by integrating genomic and epidemiological data and inferred transmission events. By repeating this analysis with weekly cumulative case data, we assessed if introductions could have been reliably inferred in real time. The number of introductions, estimated after the outbreak ended, was 19 (95% CI: 13-29), and two larger transmission clusters existed. As these introductions occurred throughout the outbreak, we conclude that the Slovenian Mpox outbreak was mainly driven by new introductions. Analysing the data 'in real time' would have only slightly overestimated the number of introductions per week, capturing the trend of introductions as main driver of the outbreak. This makes it useful for guiding control policy during outbreaks, prioritizing the rapid identification of cases among travellers, and with that preventing emergence of new transmission chains.