Temporal High-Resolution Atlas of Human Blood Leukocyte Composition in Response to Respiratory Virus Inoculation

ABSTRACT Background Respiratory viral infections produce highly variable clinical outcomes, even after controlled exposure. Human viral challenge studies are well suited to study this variation because they capture immune profiles before inoculation and across defined post-challenge intervals. However, how circulating immune-cell populations change over time, and which responses are shared or virus-specific across respiratory viruses, remains incompletely defined. Methods We leveraged HR-VILAGE-3K3M, a curated human respiratory viral challenge transcriptomic resource, to analyze longitudinal whole-blood profiles from H1N1, H3N2, RSV, and HRV challenge studies. Using statistical deconvolution and xCell-based digital sorting, we estimated changes in major leukocyte populations and 28 immune-cell subtypes in symptomatic infected (Sx/Inf) and asymptomatic uninfected (Asx/Uninf) participants. Across viruses, symptomatic infection was marked by a broad shared pattern of innate immune activation together with reduced circulating lymphocyte enrichment. Activated dendritic cells, monocytes, and neutrophils increased following challenge, whereas strong pDC activation was observed primarily in influenza studies. Most T-cell and B-cell populations decreased after challenge. Plasma-cell enrichment increased progressively over time. Despite this shared architecture, response timing differed by virus: H3N2 showed the earliest changes, followed by H1N1, whereas RSV responses were delayed and HRV showed more distinct immune-cell trajectories. Migration-associated transcriptional programs were detected across both innate and adaptive immune-cell populations, supporting coordinated immune-cell trafficking during infection. Baseline immune composition also differed between outcome groups, suggesting that pre-existing immune-state differences may influence infection outcomes. Conclusions These findings define a cellular atlas of human respiratory viral challenge responses and show that respiratory viruses induce a broadly conserved immune-response program with distinct virus-specific kinetics. This framework may help clarify immune features associated with natural resistance, symptomatic infection, and vaccine-relevant antiviral immunity.