Protect against emergent alphaviruses through computation (peac) - alphaviruses cause neurological and rheumatic diseases and pose substantial risks to human health through recurring natural…

Protect against emergent alphaviruses through computation (peac) - alphaviruses cause neurological and rheumatic diseases and pose substantial risks to human health through recurring natural outbreaks, epidemics, and the threat of bioterrorism. Some alphaviruses (e.g., eastern equine encephalitis virus and western equine encephalitis virus) are endemic in the united states, whereas others have only recently emerged domestically. Alphaviruses are transmitted through mosquitoes, and multiple factors contribute to their emergence and RE-emergence, including climate change, urbanization, and travel. The single approved vaccine against alphaviruses, ixchiq, induces only species-specific protection against chikungunya virus. However, multiple cross-reactive pan-alphavirus antibodies that can protect mice against infection by a range of alphaviruses have been identified by members of our consortium, providing templates for vaccine design. To develop broadly protective vaccines, we propose creating hetero-nanoparticles that CO-present immunogens capable of inducing broadly protective antibodies against the two complexes of alphaviruses, namely encephalitic viruses and arthritogenic viruses. Durability of the immunogen will be enhanced using an innovative approach to improve in vivo trafficking. We will further combine this b-cell targeting dual-immunogen with a broad t-cell immunogen covering all alphaviruses. Both b and t cell immunogens will be designed using novel artificial intelligence/machine learning (AI/ML)-based methods that improve upon previous approaches in terms of thermostabilization, epitope-focusing, epitope-scaffolding, germline-targeting, immunogenic t cell epitope selection and t cell epitope immunogen design. We will combine previously published AI/ML tools with our own algorithms and train new neural networks, when necessary, to develop a robust computational immunogen design pipeline. We will extensively test all immunogens in vitro and in vivo using transgenic ATX-GK mice, which carry a fully humanrepertoire, thereby more closely mimicking the human antibody-response. Deep analysis of b-cell responses by single-cell BCR sequencing will complement serological assays to iteratively improve the immunogens. The best immunogens will be validated as part of immunization and challenge studies in non-human primate models of alphavirus pathogenesis. We will employ the most advanced in silico and in vitro techniques to structurally characterize the alphavirus genus and provide public access to a curated database for structures of viral proteins, receptors, antibodies and post-translational modifications. Methods will include computational predictions (i.e., protein structures, interactions, and modifications) and experimental validation using EM polyclonal epitope mapping (empem), high-throughput cryo-electron microscopy, x-RAY crystallography and mass spectrometry. This extensive dataset will also be used to refine our AI/ML algorithms. The best immunogen will be tested in a phase i, first-in-human clinical trial by the vanderbilt vaccine research program, in partnerships with moderna INC., kcasbio, and the vanderbilt coordinating center. The proposed design is a randomized, placebo-controlled, double-blinded study to assess the safety and immunogenicity of the selected vaccine candidate. The primary objective of the phase i study will be safety and reactogenicity. Secondary objectives will also include evaluation of immunogenicity, including the potency and durability of serum antibody responses. The proposed work will combine and improve the most advanced technologies in computational biology, structural biology, vaccinology, virology and immunology to study and understand alphavirus infection and its interactions with the host immune system. We will leverage this information to develop a broad alphavirus vaccine. Our goal is to protect against emergent alphaviruses through computation (peac).