Fig. 3: Comparisons of lineage distribution and proportion of mutations associated with antibody resistance and increased infectivity in fully vaccinated and unvaccinated cases.

a, Pie charts showing the distribution of SARS-CoV-2 variant lineages in fully vaccinated and unvaccinated cases from UCSF hospitals and clinics (top row) and from Color Genomics Laboratory (bottom row). For the UCSF charts, the lighter-shaded inner circles show cases in immunocompetent patients only, while the outer circles include both immunocompetent and immunocompromised individuals. Variants carrying mutations associated with antibody resistance are highlighted in dark red boldface text. b, Pie charts showing the proportions of SARS-CoV-2 genomes carrying mutations associated with antibody resistance (L452R/Q, E484K/Q and/or F490S) and increased infectivity (N501Y/T, L452R/Q and/or F490S) in fully vaccinated (top row) and unvaccinated cases (bottom row). The pie charts include genomes corresponding to all sequenced cases containing identifiable mutations (left) and immunocompetent (middle) or immunocompromised (right) patients from UCSF hospitals and clinics. The charts are shaded according to genomes carrying ≥1 mutation associated with antibody resistance (red), ≥1 mutation associated with increased infectivity (green), or neither type of mutation (black). Fisher’s Exact test (two-tailed) was used to calculate P values. *P < 0.05, ****P < 0.0001.