Fig. 1

Schematic of experimental design. From NCBI GEO, we identified gene expression microarray datasets from influenza viral challenge studies and studies of naturally acquired infection. Using immunoStates cell mixture deconvolution, we estimated the immune cell proportions in each sample. We separated the challenge studies into discovery and validation cohorts. We analyzed differences at baseline between symptomatic shedders and asymptomatic nonshedders using MetaIntegrator, a meta-analysis framework. We identified immune cell types with significantly different proportions between symptomatic shedders and asymptomatic nonshedders, which we further investigated in an influenza challenge validation cohort, and cohorts of naturally acquired acute infections