Fig. 1: CXCL10 mRNA levels can be measured as a proxy for T cell activation.

a, Schematic of workflow for the T cell activation assays. All assays begin with whole-blood collection followed by overnight stimulation with DMSO, nucleocapsid (NP) or SpG peptide pools. Next, supernatants are collected for ELLA or Olink; RNA is extracted and used for probe-based qPCR (qTACT) or next-generation sequencing (TACTseq) or whole blood is diluted and used directly for qPCR (dqTACT). Figure created with Biorender.com. b, CXCL10 is upregulated in response to spike peptide pool activation of whole blood. Volcano plot displaying differentially expressed genes stimulated by the spike peptide pool versus DMSO, grouped by the participant’s COVID-19 or vaccination status, displayed as red (upregulated) or blue (downregulated). Significantly differentially expressed genes were defined as having an adjusted P value <0.05 and |log₂FC| > 1. P values were calculated using DESeq2 (two-sided) and adjusted using the Benjamini–Hochberg method. c, CXCL10 and IFNG mRNA induction correlate. Scatter plot displaying each gene's correlation to IFNG expression across samples (x axis), and the corresponding log₂FC (calculated by DESeq2) for the spike peptide pool versus DMSO, grouped by COVID-19 or vaccination status. Correlation calculated using Spearman’s index. d, Venn diagram displaying overlap in significantly upregulated genes in convalescent and vaccinated participants for spike peptide-stimulated samples compared to DMSO control samples. Significantly upregulated genes were defined as having P < 0.05 and log₂FC > 1. e, GSEA plot displaying significantly positive enrichment for IFN-γ response genes among the upregulated genes in spike peptide simulate samples compared to DMSO control samples in COVID-19 convalescent and vaccinated cohorts.