Fig. 2.

Spatially explicit phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. (A) Continuous phylogeographic reconstruction performed along each Belgian clade (cluster) identified by the initial discrete phylogeographic analysis. For each clade, we mapped the maximum clade credibility (MCC) tree and overall 80% highest posterior density (HPD) regions reflecting the uncertainty related to the phylogeographic inference. MCC trees and 80% HPD regions are based on 1,000 trees subsampled from each post burn-in posterior distribution. MCC tree nodes were colored according to their time of occurrence, and 80% HPD regions were computed for successive time layers and then superimposed using the same color scale reflecting time. Continuous phylogeographic reconstructions were only performed along Belgian clades linking at least three sampled sequences for which the geographic origin was known (see the detailed analytical pipeline in Supplementary Information for further detail). Besides the phylogenetic branches of MCC trees obtained by continuous phylogeographic inference, we also mapped sampled sequences belonging to clades linking less than three geo-referenced sequences. Furthermore, when a clade only gathers two geo-referenced sequences, we highlighted the phylogenetic link between these two sequences with a dashed curve connecting them. Subnational province borders are represented by white lines. (B) MCC tree branches occurring before March 18, 2020 (beginning of the lockdown). (C) MCC tree branches occurring after March 18, 2020. See also supplementary figure S2, Supplementary Material online, for a zoomed version of the dispersal history of viral lineages in the Province of Liège, for which we have a particularly dense sampling.