The spatial landscape of infectious mononucleosis tonsils

Abstract

Primary Epstein-Barr virus (EBV) infection remains incompletely understood, particularly in relation to the nature of in vivo latency patterns and their influence on the immune microenvironment. Here, we present the first multiomic single-cell spatial atlas of palatine tonsils from individuals with infectious mononucleosis (IM). We identify rare EBV infection of epithelial cells, challenging the prevailing assumption that primary infection is restricted to B- and T-cells. Moreover, our detailed analysis suggests a spatiotemporal transition of EBV latency programs, with distinct viral gene expression patterns corresponding to specific tissue microenvironments-a dynamic process previously inferred but not directly mapped in human tissues. We found that cells expressing the EBV-encoded protein LMP1 form an immunosuppressive niche that is rich in IDO1+PDL1+ macrophages and relatively depleted of T-cells. Furthermore, the T-cells that do infiltrate LMP1+ regions exhibit signatures consistent with an activated and cytotoxic phenotype, providing new insights into how LMP1 shapes immune evasion. Taken together, our data redefine the spatial and functional organisation of primary EBV infection, integrating latency plasticity, epithelial tropism, and microenvironmental immunosuppression into a unified framework, as well as providing a data-rich framework for understanding viral persistence and immune evasion.