(A) Dynamic genes and pathways identified through GAMM and TcGSA, respectively. (B) Spaghetti plots depicting time trends of a dynamic antiviral pathway identified through TcGSA. Colored solid lines represent the scaled median expression of one gene across all participants, and black dotted lines represent the smoothed median of all genes for a given time trend. Colors denote genes in distinct time trend clusters (blue, cluster 1; pink, cluster 2). (C) Pearson’s correlation matrix of genes with ≥0.3 absolute correlation coefficient with SARS-CoV-2 VL in temporally aligned blood and swab samples. (D) Temporal kinetics of SARS-CoV-2 VL and genes showing moderate-to-strong associations with VL in previously vaccinated and unvaccinated COVID-19⁺ participants. Solid lines represent generalized additive model smoothing across all participants within a group, and colored shades represent the 95% confidence interval. Green, red, and blue colors denote healthy, COVID-19⁺ unvaccinated, and COVID-19⁺ vaccinated participants, respectively. Dotted lines represent individual temporal trajectories of gene. (E) Temporal kinetics of IFI27 gene expression, VL, and symptom burden in individual participants.