Fig 1.
Temporal dynamics of SARS-CoV-2 fitness, as characterized by Geno-GNN.
(A) Fluctuate-rise-stabilize pattern of angiotensin-converting enzyme 2 (ACE2) binding affinity. Horizontal colored dashed lines represent the experimental ACE2 binding affinity for each variant as measured by deep mutational scanning (DMS) [47,48] (values shown in parentheses). ACE2 binding affinities for variants BQ.1.1, XBB.1.5, EG.5.1 and BA.2.86 were used for external validation. (B) Stepwise pattern of immune escape against the wild-type (WT) convalescent immunity type. (C) Stepwise pattern of immune escape against the WT vaccine immunity type. The x-axis represents the monthly time points from March 2020 to February 2024, and the left y-axis represents the average fitness values of sampled sequences. Shaded gray regions highlight periods of rapid fitness increases, and corresponding fitness differences are indicated. Color gradients represent the predominant variant for each month, defined as the variant with the highest percentage in a given month (S5 Fig).
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).
Fig 3.
SARS-CoV-2 fitness trajectory, as revealed by Geno-GNN.
(A) Distribution of RBD mutations across major epidemic variants, including BA.1, BA.2, BA.4/5, BQ.1, XBB.1.5, XBB.1.9, and EG.5.1. Fixed mutations, shared by multiple variants, are highlighted. The x-axis represents mutation types; for loci with multiple mutations, specific types are displayed in the corresponding cell. (B) Fitness trajectories of SARS-CoV-2 identified through virtual mutation scanning. ACE2 binding affinities are grouped by the number of mutations and the number of immune types that escaped. Major real-world variants are denoted by white rhombuses. Color gradient represents the number of escaped immune types. Black dashed line indicates the ACE2 affinity of the wild type. “All mutations” refers to the complete set of RBD mutations in major variants relative to the wild-type strain, defining the combinatorial mutation space. Fixed mutations are regarded as a single mutation and assumed to co-occur or co-disappear in virtual mutation scanning. (C) Differentiation of two distinct trajectories based on fixed mutations. ACE2 binding affinities are categorized by the number of immune types escaped (IT: immune type). Median ACE2 affinities for intermediates with and without fixed mutations are indicated by blue and red dashed lines, respectively. Bar chart presents the number of intermediates in each immune type. Boxplots compare ACE2 affinities for intermediates with and without fixed mutations; statistical significance is annotated. Boxes represent the interquartile range (25th–75th percentiles), and whiskers extend to 1.5 times the interquartile range. Fixed mutations are shown in color.
Fig 4.
Quantification of the fitness effects of mutations in major circulating variants within the combinatorial mutation landscape, according to Geno-GNN.
(A) Contributions of nonfixed mutations to ACE2 affinity (upper panel) and immune escape (lower panel, conval: convalescent). (B) Contributions of fixed mutations to ACE2 affinity (right panel) and immune escape (left panel). Heatmap color scale indicates the extent of immune escape attributed to each mutation. White represents the absence of a contribution to immune escape for a given immune type. In bar plots, red bars indicate an increase in ACE2 affinity, whereas blue bars indicate a decrease. “Δ ACE2 affinity” represents the difference in the median ACE2 binding affinity between receptor binding domain (RBD) sequences with and without the mutation.