Fig. 3

High-Throughput genomic surveillance allows the identification of new SARS-CoV-2 lineages. A Donut chart representing the amount of analyzed genomes presenting the Spike E484K mutation, divided by lineage. The definition of Expected lineage is described in the Methods. B Section of the phylogenetic tree representation of the whole dataset (n=12,998), colored by lineages. The identified lineage is reported (blue dots, left) and zoomed in (right). n:sample size. C Geographic distribution of genomic variants belonging to the identified lineage, colored by the collection date. The size of each pie chart is proportional to the number of samples in each geographic position. n:sample size. D Line plot showing the frequency trend of the selected mutations in time. E Section of the phylogenetic tree representation of the whole dataset (n=12,998), colored by lineages. The identified lineage is reported (arrow, blue dots). n:sample size. F Geographic distribution of genomic variants belonging to the identified lineage, colored by the collection date. The size of each pie chart is proportional to the number of samples in each geographic position. n:sample size. G Genomic characterization of twenty patients with long COVID-19 infection. The number of detected mutations is reported as a function of the number of days from the first swab. The assigned lineage (colors) and consistency (transparency) are also displayed. H Patient 8 genomic characterization relative to the number of detected mutations (colors), the infection load (y-axis), and symptoms severity (+++: severe; ++: moderate)