Project Summary Human enterovirus (HEV) infections primarily affect infant and adolescent populations, causing a wide range of clinical manifestations that commonly include respiratory illness and mucocutaneous lesions, or hand, foot and mouth disease. In some cases, the infection is life- threatening. The clinical manifestations are a function of their tropism. For example, some HEVs, including EV-A71 and EV-D68, are associated with serious neurological symptoms due to invasion and damage of central nervous tissues. Others, such CVB3, are implicated in respiratory symptoms and cardiomyopathy. This proposal aims to take an integrative approach to understand how tissues, and cells within these tissues, respond to infection by CVB3 and the emerging pathogens EV-D68 and EV-A71. We will determine the temporal and spatial dynamics of HEV infection using recent advances in genomics: (i) We will profile single-cell transcriptomes to quantify viral replication levels and the host response to infection across cells and tissues over the course of infection. (ii) Given that intra-host adaptation appears to be important in infection, in parallel, we will map the mutational spectrum of the replicating viruses using a novel ultra-deep sequencing approach. We will use new innovative technologies, such as ultra-deep virus population sequencing, deep learning and single-cell analysis to increase our basic understanding of the pathogenesis of enteroviruses A, B and D. Finally, given that innate immunity is a major determinant of tissue tropism, we will use mice with deletions of specific type-I IFN subtypes to determine the significance of interferon diversity in controlling HEV infections. These data will enable us to determine cell types that HEVs infect, the response that the host mounts against them in each cell and tissue, and the viral mutants that emerge in different tissues. Understanding pathogenesis is critically needed for developing effective and broadly-acting countermeasures and to inform the development of effective and broad-spectrum vaccines and antiviral compounds.

Enteroviruses are a major source for disease and hospitalization, but currently little is known about their mechanism of infection and there is no available treatment. Using recent advances in single-cell transcriptomics and ultra-deep virus population sequencing, we will explore the dynamics of in vivo enterovirus infection and the host response to it across cells and tissues. Combining these strategies with animal models defective in specific antiviral pathways, we will gain mechanistic insights into viral spread and pathogenesis, which is critical to develop effective antiviral drugs and vaccines.