Figure
Upper panel: maximum likelihood unrooted tree with genetic distances of the three identified strains (highlighted as coloured circles within the phylogenetic tree; Strain 1 in orange, Strains 1 + 2 in ochre, and Strain 3 in purple) based on sequence alignment of 2,249 positive SARS-CoV-2 samples from cases among the Madrid population throughout the pandemic. Coloured branches are used for SARS-CoV-2 sequences from specimens collected during the first COVID-19 wave (black) and after July 2020 (grey). The B.1.1.7 variant is showed purple.
Lower panel: location of single nucleotide polymorphisms along the SARS-CoV-2 reference genome for the three identified strains. Relative allele frequency of each strain (Strains 1 and 2; See also Supplementary table) in the superinfection event is indicated for the positions with heterozygous calls. Fasta files were deposited in GISAID (accession numbers strain 1 - EPI_ISL_1547368 strain 2 - EPI_ISL_1547369 and strain 3 - EPI_ISL_1547363).