Core E: Phylogenetic and mutational scanning

PROJECT SUMMARY – CORE E: PHYLOGENETIC AND MUTATIONAL SCANNING This Core will use cutting-edge experimental and computational techniques to ensure that the vaccines target the full relevant evolutionary breadth of the prototype virus families, and to map the breadth and specificity of vaccine-elicited antibody responses. To do this, the Core will combine sequencing and phylogenetic analyses

with deep mutational scanning to characterize viral diversity and its impact on the vaccines. First, existing sequence data on each of the prototype viruses will be integrated into the nextstrain platform to facilitate easy surveillance and phylogenetic analyses. These data will then be used to inform the creation of phylogenetic

and deep mutational scanning libraries to experimentally characterize the natural and possible future mutational diversity of the key viral glycoproteins. The libraries will utilize a powerful new pseudotyped lentiviral deep mutational scanning system that enables variants of any viral entry glycoprotein to be characterized at

high-throughput using safe non-replicative virions at biosafety level 2. For each prototype viral entry glycoprotein, the Core will create two types of libraries: phylogenetic libraries that contain variants spanning the natural diversity of that virus, and deep mutational scanning libraries that contain all amino-acid mutants of key

representatives of each virus. These pseudotyped lentiviral libraries will be used to characterize how all natural and mutational variants of the viral glycoproteins mediate entry in cell culture, and are recognized by monoclonal and polyclonal serum antibodies. Initially, the resulting information will inform the design and

testing of the immunogens in the Center Projects. Then as these immunogens proceed into testing, the libraries will be used to map the specificity and breadth of the elicited neutralizing responses. Taken together, this Core will therefore provide a resource that can inform the Center Projects through all steps from initial

immunogen design to characterization of vaccine-elicited responses.