Fig. 1

Sequencing rate and lineage dynamics. Each row corresponds to the region highlighted to the far left. The two vertical dashed lines indicate the beginning and end of study period used to infer B.1.1.7 transmissibility, while the non-shaded area shows the period used for phylogenetic analysis. The time outside the study are shaded in gray. A Sequencing rate across time. Total height corresponds to the total number of cases for each week. Green bars indicate the number of cases for which a high-quality genome was available (less than 3000 ambiguous bases). B Relative abundance of ten most abundant PANGO lineages across Denmark in the study period. Computed from rolling averages of daily cases with genome available over a 14-days window. Less abundant lineages are not shown but included in the unfilled area of the plots. The black dot and date corresponds to the point where B.1.1.7 crosses 50% relative abundance