Screening was performed with the TaqMan™ SARS-CoV-2 mutation panel molecular assay (ThermoFisher Scientific, Massachusetts, USA). For each mutation of interest, probes labelled with VIC or FAM detect the wild type (WT) and the mutated sequence, respectively. WT samples are represented as red dots along the x-axis and mutated samples as blue dots along the y-axis. A dual population is suspected by intermediate mutation profile with detection of WT and mutated sequences in the same sample and is represented by green dots. The figure at the bottom represents the variant allele frequency clade-defining mutations for 21J Delta and 21K Omicron along the SARS-CoV-2 genome for one patient (P6). Mutations are represented with the variant allele frequency on the first Y axis and the depth of each genomic position on the secondary Y axis. Recombination points are indicated by blue arrows and were confirmed by Single Molecule Real Time sequencing.Abbreviations: SNP, Single Nucleotide Polymorphism