Fig. 3: Persistent lineages within Southeastern Asia and their topological and temporal distributions under the even sub-sampling scheme.

a Schematic diagram illustrating how viruses circulating in Southeastern Asia belonging to persistent lineages were identified. A Southeastern-Asia tip was defined as belonging to a persistent lineage if its nearest trunk node was associated with “Southeastern-Asia” and all ancestor nodes from this tip to the nearest trunk node were associated with “Southeastern-Asia” backwards in time. Trunk was defined as all branches ancestral to viruses sampled within 1 year of the most recent sample. b, c The maximum clade credibility (MCC) tree of A/H3N2 and B/Victoria lineages. Tips are coloured by geographic region of virus collection, in which strains in Southeastern Asia are separately annotated as belonging to persistent or non-persistent lineages; internal branches are coloured by geographic region as inferred by Bayesian phylogeographic methods. Trunk nodes over time are presented as dots coloured by trunk location on a horizontal line at the top of the panels. Trunk assignments are summarised up to the most recent common ancestor (tMRCA) of viruses sampled within 1 year of the most recent sample. d, e The temporal distribution of the numbers of sub-sampled virus genomes from Southeastern Asia belonging to persistent and non-persistent lineages over influenza seasons, for A/H3N2 and B/Victoria lineages, respectively (left y-axis). The proportion of virus sequences belonging to persistent lineages over time is represented by the grey line (right y-axis).