Figure 2
Lineage distribution per week and positive samples detected (discontinuous line) from March 2020 to February 2022 in Barcelona, Spain. Defective genomes are shown below the lineage distribution in bar plots starting from the first patients detected in March 2020: B.1.5 (yellow), B.1.1 (dark green), B.1.177 (violet), Alpha (light green), Beta (pink), Delta (blue), and Omicron (black). The bar plots below each variant indicate defective deletions in amplicon A78 in the 78 patients studied at the nucleotide level. The box located in the left corner are the defective bar plots related to patients in March 20201. The x-axis provides the multiple alignment (MA) nucleotide positions and the amplitude of the deletions by subregions, and the y-axis shows the frequency of the deletion (percentage) on the right and the number of reads on the left. As no insertions causing defective genomes were observed, the MA positions correspond to S gene positions. Dashed lines indicate the S1/S2 (left) and S2’ (right) cleavage sites. Detailed bar plots for the 78 patients by amplicon are provided in supplementary figures (Supplementary Figures S2A−2G for deletions and 3A-3G for defective deletions).
