Fig. 1

SARS-CoV-2 lineages identified in patient RNA samples (n = 210) and the comparison to lineages reported in the state of Illinois during the same period. Patient samples (phylogenetic tree) are annotated with different clade colors representing variants from Delta to Omicron BA.1 to BA.5 (except for one Alpha, P1, that was collected in May 2021 and serves as a positive control for sequencing). The outside color strip indicates the sample collection time from November 2021 (light blue) to November 2022 (dark blue). The inner ring shows lineages identified in Illinois with months annotated inside of the circle; sublineages > 10% frequency are shown in the representative color scheme, and lineages < 10% frequency are included in “other” in gray