Exploiting virus and host diversity to define mechanisms of cross-species infections

Abstract Emerging viruses represent a major public health threat. This is evidenced by several zoonotic events over the last ~100 years including 1918 influenza, human immunodeficiency virus, Ebola, Zika, SARS-CoV-2, SARS- CoV-2, among others. Reemerging viruses like Dengue, West Nile, and Chikungunya also pose significant risks and the geographical range of these viruses are continuing to expand. This results in new regions becoming endemic exposing new species. The rate of virus emergence and reemergence is on the rise due to the expanding human population, land use change, and movement of animals into new habitats. Currently, we cannot predict which species are permissive and may become reservoirs in new geographical environments. Increased geographical and host range of viruses increases the odds of spillover into humans. Virus are obligate intracellular parasites that require use of host factors to complete their lifecycle. Viruses also must evade the potent antiviral immune responses which have evolved to sense and protect against virus infections. Both pro- and anti-viral host factors are under heavy selection from viruses, and their genetic sequences can vary significantly across hosts. Understanding species-specific susceptibility is essential for predicting spillover events, identifying new reservoirs, and guiding public health interventions. Furthermore, a better understanding of virus-host interactions that impact replication may also lead to new antiviral treatments. The goal of this P01 Program Project is to determine the host factors that control infection of alphaviruses and flaviviruses across mammals. We will leverage a novel resource called the "Fibroblast Zoo" which is comprised of primary dermal fibroblasts which currently contains 89 mammalian species. Fibroblasts are a relevant cell type because they are an early target of virus infection after transmission by a vector during a bloodmeal and play critical roles in sensing infection and spreading virus. While they are not an intact animal, we suggest that fibroblasts can be used as a powerful screening tool to evaluate genetic landscape of virus host interactions across diverse species. We will evaluate both pro- and anti-viral factors that govern host range across two research projects. Project 1 will reveal conserved and divergent host factors that promote infection of alphavirus and flaviviruses across species. Project 2 studies will reveal conserved and divergent mechanisms of 1) innate immune and IFN effectors, 2) alphavirus and flavivirus control, and 3) viral evasion across species. These projects will be supported by three cores, the Administrative Core (Core A) will oversee the P01 Program, Core B will distribute fibroblasts from diverse species and viruses, and generate infectivity data, and Core C will perform transcriptome and genome sequencing as well as sophisticated computational analyses. Together the linked results from the projects and cores will define mechanisms that drive cellular susceptibility to virus infections across diverse species and will inform consideration of spillover potential, and strategies for mitigating infection and disrupting zoonotic virus transmission.