Project Summary - Project 2 The objective of Project 2 is to investigate the complex interplay of virus genetics and host immunity in determining epidemiology and outcome of infection with Lassa virus, Ebola virus, and SARS-CoV-2. Our central hypothesis is that both host and virus factors play key roles in determining the severity of clinical outcomes including survival, disease severity and the development of long-term sequelae. To test this hypothesis, we will investigate viral genetics, development of host immunity, and how these processes interact as a result of viral infection or vaccination. In focusing on the host-pathogen interface, we will complement the host-focused studies from Project 1 to better understand the complex factors that determine the clinical outcome and epidemiology of Lassa, Ebola, and COVID-19. To accomplish this, we will complete the following: In Aim 1, we will refine viral sequencing techniques to generate large catalogs of Lassa virus and SARS-CoV-2 genomic diversity. We will then integrate these data with environmental and demographic data and apply phylodynamic models to identify virus mutations and variants most likely to have an effect on disease severity. In Aim 2, we will perform single cell sequencing and transcriptomics to deeply characterize the evolution of adaptive immunity in response to acute Lassa virus infection or vaccination. We will also isolate monoclonal antibodies from individuals previously infected with or vaccinated against Lassa virus, Ebola virus, or SARS-CoV-2 to understand the diversity of the human humoral response. In Aim 3, we will extend the multi-omics work proposed in Aim 2 to individuals infected with different viral variants, with the goal of developing a predictive model of immune response and clinical outcome. This model will integrate the systems serology data from Project 1 as part of a framework of repeated cycles of experimental data generation, integration, application, validation, and refinement to identify predictive biological markers of human disease and outbreak dynamics. Finally, in Aim 4, we will validate the findings from the previous aims in a BSL-4 setting (the biosafety level required for working with live Ebola or Lassa virus) and use the results of animal models to further refine our predictive models of clinical outcome.