homeRNA self-blood collection by exposed close contacts enables high-frequency temporal profiling of the pre-symptomatic host immune kinetics to respiratory viral infection

BACKGROUND: Host immunity is critical in determining outcomes of acute respiratory viral infections (ARVIs). However, detailed kinetics of host immune responses following natural exposures are poorly understood. Investigating the host response during the pre-symptomatic phase of viral infection is challenging, and prior work has largely relied on human challenge studies. In this prospective longitudinal study, we utilized a self-blood collection tool (homeRNA) to profile the host response during pre-symptomatic ARVIs in recently exposed adults and present a study framework for the conduct of large-scale longitudinal mechanistic studies. METHODS: We prospectively recruited non-symptomatic adults with recent exposure to ARVIs who subsequently tested negative (exposed uninfected) and positive for respiratory pathogens. Study participants performed self-collection of blood and nasal swabs across a 4-week observation window. Daily monitoring of symptoms, viral load, and blood transcriptional responses was performed for the first week followed by weekly monitoring of blood transcriptional responses and symptoms. Nasal swabs were assayed for respiratory pathogens including SARS-CoV-2. Immune kinetics from 132 longitudinal blood samples (8 SARS-CoV-2 infected and 4 exposed uninfected) were profiled at high temporal resolution for 773 host response genes. FINDINGS: 68 participants across 26 U.S. states completed the study between June 2021 – April 2022, with 97.6% of scheduled longitudinal blood collections (n=691), 97.9% of nasal swabs (n=466) and 97.2% of symptom surveys (n=688) returned. SARS-CoV-2 infection was confirmed in 25% of the participants (n=17) Expression of host immediate early genes (IEGs) involved in AP-1 transcriptional complex and prostaglandin biosynthesis along with genes encoding the early T-cell activation antigen (CD69), pyrogenic cytokines (IL-6, MIP-1β, and IFN-γ), cytotoxic cell receptors and granule proteins, and interferon-induced GTPases were detected in the periphery prior to onset of viral shedding in the nasal passage. Upon onset of viral shedding, robust induction of interferon stimulated genes (ISGs) were observed. We also observed elevated expression of the host defense peptides DEFA4, LCN2, LTF, BPI (HDPs) in exposed uninfected individuals. INTERPRETATION: Signatures of T-cell responses prior to nasal viral shedding followed by robust induction of innate ISGs upon onset of viral shedding suggests that T-cell derived immune memory may play a role in pathogen control during early phases of the infection. Elevated levels of HDPs in exposed uninfected individuals suggest a potential role for neutrophil-mediated immunity in host defense during pathogen exposure. Finally, we demonstrated that unsupervised self-collection and stabilization of blood using homeRNA can be used to study early host immune kinetics to natural ARVIs at a temporal resolution comparable to that of human challenge studies.