Extended Data Fig. 2: Phylogenetic relationships between nOPV2 ES isolates from Uganda.

Phylogenetic trees with all nOPV2 sequences from ES samples were constructed using the FastTree algorithm (version 2.1.11) within Geneious. Sequence alignment was first generated using MUSCLE, and trees were inferred under the generalized time-reversible (GTR) model with CAT approximation for rate heterogeneity across sites. FastTree constructs an initial tree using a neighbor-joining heuristic, followed by maximum-likelihood optimization with nearest-neighbor interchanges (NNIs) to refine topology and branch lengths. Trees were visualized and annotated using Geneious Tree Viewer. The scale bar represents substitutions per site. Two small genetic clusters (in blue and green in the tree) were identified.