Fig. 5: Maximum clade credibility phylogeny for subtree A, representing diversity of lineages A.23 and A.23.1. | Nature Communications

Fig. 5: Maximum clade credibility phylogeny for subtree A, representing diversity of lineages A.23 and A.23.1.

From: Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

Fig. 5

The phylogeny with associated ancestral locations was inferred using travel history-aware asymmetric discrete state phylogeographic inference. A total of 33 locations were considered in the analysis but are grouped for visualization purposes. The branches in the phylogeny are colored according to the geographical location of the reconstructed ancestral regions. Rwandan sequences are indicated as large tips, colored by associated travel histories (available for 11 of the Rwandan sequences). The travel history-aware phylogeographic reconstruction on subtree A infers frequent mixing between Rwanda, Uganda, and Kenya, with the latter seeing introduction events from both Uganda and Rwanda. Both Kenya and Uganda are estimated to have seeded introductions into Tanzania, with the former also seeding an introduction into South Sudan. Importantly, the travel history-aware approach includes (returning infections from) Tanzania in lineage A.23.1, which could not be inferred via other phylogeographic approaches.

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