Fig. 3: Phylogenetic tree and APOBEC3 mutational profile of the Irish MPXV clade Ia genome imported from the Democratic Republic of the Congo.

A The maximum likelihood phylogenetic tree including the Irish sequence and clade I sequences downloaded from GISAID and PathoPlexus (n = 957). Clade Ia sequences are shown in blue, with those from the Kinshasa 2024 outbreak (sh2024) highlighted in pink. The subcluster containing the Irish sequence is marked by green diamonds. Clade Ib sequences are collapsed and represented by a grey triangle. Branch support values (bootstrap percentages) are shown at the nodes. The scale bar indicates the substitution rate per site (subs/site). B A zoomed-in view of the phylogenetic subcluster containing the Irish sequence, showing individual mutations along each branch. Mutations are represented as boxes, coloured by type: putative APOBEC3-induced mutations (TC → TT on the leading and GA → AA on the lagging strand) are shown in orange, and all other single-nucleotide variants (SNV) are shown in yellow. This subcluster includes 21 sequences from the sh2024 outbreak, including the Irish case. For additional context, one sequence from the broader sh2024 outbreak cluster (pink) that falls outside this subcluster, as well as one clade Ia sequence (blue), are also shown.