Extended Data Fig. 4: Analysis of non-polio enterovirus C VP1 sequences from Uganda.

Phylogenetic relationships between VP1 nucleotide sequences of species C enterovirus strains from serotypes known to frequently recombine with poliovirus identified in sewage samples from the Kisenyi Sewage Ponds site in Kabarole (Uganda). Phylogenetic trees 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. VP1 sequences from Ugandan strains in this study are shown in red text in panel A and analysed alone in panel B.