Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning
Fig 2
Heterogeneity in SARS-CoV-2 fitness dynamics across immune backgrounds.
(A–C) Temporal trends in angiotensin-converting enzyme 2 (ACE2) binding affinity (A) and immune escape against the wild-type (WT) convalescent (B) and WT vaccine (C) backgrounds, stratified by vaccine type. Shaded regions indicate variant transition periods: T1 (Others-to-Alpha) and T2 (Alpha-to-Delta). (D, E) Fitness change rates across regions with different vaccine backgrounds during the Others-to-Alpha (D) and Alpha-to-Delta (E) transition periods. The y-axis represents estimated slopes (i.e., fitness change rates) with 95% confidence intervals (black error bars). p values are indicated: *p < 0.10; **p < 0.05; ***p < 0.01; ****p < 0.001; NS, not significant. (F, G) Statistical validation of the associations between fitness change rates and immune backgrounds during the Others-to-Alpha (F) and Alpha-to-Delta (G) transition periods. The x-axis represents p values from the observed slope comparisons, whereas the y-axis represents mean p values from 100 random permutations with 95% confidence intervals. Shapes correspond to the compared immune backgrounds, and colors indicate fitness types. Horizontal and vertical dashed lines indicate the significance threshold (0.1).