Extended Data Fig. 8: Phylodynamic estimates of the effective reproductive number (Re) of Spanish SEC7.

A birth–death skyline (BDSKY) model was implemented in Beast v.2, allowing for piecewise changes in Re, with the time and magnitude estimated from the data. The X axis represents time, starting with the MRCA of all sampled diversity within SEC7 and ending with the date of the most recently sequenced genome from 15th May. The blue dotted line indicates the posterior value of the timing of a most important decrease in Re, around 20th March 2020 [95% HPD: 15–25th March]. The Y axis represents Re, and the violin plots show the posterior probability distribution for this parameter before and after the change time in Re; with a mean of 2.10 [95% HPD: 1.67–2.62] and 0.27 [95% HPD:0.06–0.47] before and after this time, respectively. The phylogenetic tree in the background is the maximum clade credibility tree from the BDSKY analysis, with the tips colored according to whether they were sampled before or after 20th March. The lower whisker, higher whisker, center and bounds of each boxplot refers to quartile 1–1.5 interquartile range, quartile 3 + 1.5 interquartile range, mean, first and third quartiles of the data. Individual points are outliers (values lower than quartile 1–1.5 interquartile range and higher than quartile 3 + 1.5 interquartile range). Boxplot was constructed with all the Spanish sequences in SEC7 (N = 182).