Extended Data Fig. 9: Comparison between strains carrying 614D and 614 G mutations.

a. Number of sequences belonging to SEC7, SEC8 (614D) and those having the 614 G allele. b. Phylodynamic estimates of the effective reproductive number (Re) of clades harboring 614D mutation (SEC7 and SEC8) and Pango lineages with 614 G mutation (B.1 and B1.1). 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 violin plots show the posterior probability distribution (HPD) interval for Re parameter before (Re1) and after (Re2) the changing time estimates (dotted line). For SEC7, Re1: 2.10 [95% HPD: 1.67–2.62] and Re2: 0.27 [95% HPD:0.06–0.47]; changing time 20th March 2020 [95% HPD: 15–25th March]. For SEC8, Re1: 3.14 [95% HPD: 2.71–3.57] and Re2: 0.23 [95% HPD: 0.15–0.32]; changing time 9th March 2020 [95% HPD: 8–10th March]. For B.1, Re1: 1.86 [1.6–2.16] and Re2: 0.26 [0.14–0.41]; changing time 23rd March 2020 [95% HPD: 21–25th March]. For B.1.1, Re1: 1.62 [1.44–1.80] and Re2: 0.15 [0.05–0.29]; changing time 10th April 2020 [95% HPD: 9–12th April]. 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). Boxplots were constructed with all the Spanish sequences in SEC7 (N = 182), SEC8 (N = 636), B.1 (N = 191) and B.1.1 (N = 223).