Fig. 3: SEC8 epidemiological success and impact of mobility restrictions.
a, ML phylogeny with all strains of SEC8. Samples with epidemiological evidence about their origin are marked in the tree. In red, cases imported from different events in Italy. In orange, secondary cases originated from one of the cases introduced from Italy (also marked with blue arrows). In purple, cases related to a large funeral in La Rioja. Green stars mark potential superspreading events of more than ten sequences sharing at least one clade-defining SNP. b, Contribution of SEC8 to the total of samples sequenced over time. The horizontal red line marks the start of the Spanish lockdown on 14 March 2020. c, Phylodynamic estimates of the reproductive number (Re) of SEC8. The x axis represents time, from the origin of the sampled diversity of SEC8 to the date of the last collected genome on 16 May 2020. The blue dotted line shows the posterior value of the timing of the most important change in Re, around 9 March 2020 [95% HPD: 8–10 March]. The y axis represents Re, and the violin plots show the posterior distribution of this parameter before and after the change time in Re, with a mean of 3.14 [95% HPD: 2.71–3.57] and 0.23 [95% HPD: 0.15–0.32] before and after the change time, respectively. The phylogenetic tree in the background is a maximum clade credibility tree with the tips colored according to whether they were sampled before or after 9 March 2020. 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 SEC8 (N = 636).
