FIGURE 1.

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 2249 positive severe acute respiratory syndrome coronavirus 2 (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 ($\mathrm{grey}$). The B.1.1.7 variant is shown in 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 Table S1) 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). FASTQ files were deposited at the European Nucleotide Archive (https://www.ebi.ac.uk; project reference: PRJEB47864)