Dynamic local T cell responses underlie associations in disease severity during infant RSV infection

Abstract Respiratory syncytial virus (RSV) infections are common throughout infancy, resulting in a wide range of clinical manifestations, with significant morbidity and mortality seen worldwide. The mechanisms leading to severe disease remain unknown. We sought to determine viral and immune mediated factors related to disease severity. Utilizing multi-parameter flow cytometry and single cell RNA sequencing, we correlated local T cell responses with dynamic changes to viral load in samples obtained from infants infected with RSV. Viral burden was highest at time of study enrollment and declined towards clearance in all subjects regardless of disease severity. Peak CD8 T cell response occurred several days after peak viral burden. Disease severity was associated with the accumulation of highly proliferative CD25+/Ki67+ CD8 T effector memory cells in the respiratory tract. Single cell RNA sequencing of T cells revealed distinct transcriptomic profiles of T cell populations. Respiratory tract CD8 T cells upregulated genes for granzyme, perforin, and tissue adhesion (CXCR6, CD49a) while CD4 T cells in the airway were enriched for regulatory T cell genes (FoxP3, CTLA4) compared to blood. Blood samples were defined primarily by gene signatures associated with naïve T cells and no significant upregulation of effector genes, emphasizing the compartmentalized nature of the immune response. Interestingly, clusters of gamma delta T cells upregulating AREG were found in airway samples, supporting a role for immune mediated tissue repair. These results show that disease severity during RSV infection in infancy is associated with localized immune responses and provide insights into how tissue repair may be mediated following severe disease.