Recoding the SARS-CoV-2 genome - A multidisciplinary approach to generate live-attenuated coronavirus vaccines

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The newly discovered coronavirus (CoV) SARS-CoV-2 is responsible for the recent pandemic of upper respiratory disease and pneumonia that threatens countless lives across the globe. Like all viruses it critically relies on reprogramming of the cellular metabolism, in particular on hijacking the translation machinery of its host. The goal of this proposal is to identify vulnerabilities of the virus during its usurpation of the host cell. Specifically, we will comprehensively test multiple aspects that SARS-CoV-2 may use to hijack host translation. We will use this knowledge to rationally design re-coded coronavirus genomes in order to develop novel live-attenuated coronavirus vaccines. This strategy will not only be applicable for this virus but also for newly emerging zoonotic viruses in the future.Therefore, we will first ask whether the virus hijacks the host RNA modifications machinery to modify its own RNA genome to avoid detection by the host cell’s innate immune defense systems. Second, we will identify the host RNA modification machinery that mediates the modification of the viral genome. Third, we will examine whether viral RNA modifications facilitate the recruitment of the host translation machinery. To this end, we will use ribosome profiling and RNAseq in a high-resolution infection time course to quantitatively determine the translational response of the host cell. This will reveal how SARS-CoV-2 exploits the mRNA translation machinery of the host during its life cycle. Fourth, we will test whether the virus modulates the levels of tRNA and tRNA modifications to achieve efficient translation despite the diverging codon usage between its genome and the one of its host. Fifth, we will apply the knowledge gained to develop a series of synthetic attenuated viruses lacking, for example, RNA modifications or containing sequence elements that are difficult to translate during an infection. We will analyze the generated virus constructs both in vitro and in vivo and test selected viruses by ribosome profiling and in animal models. By combining these approaches, we will identify how SARS-CoV-2 interacts with ist host and in particular its translation and RNA modification machineries. This will identify attenuated virus variants as well as drug targets and strategies to rationally design attenuated viruses that can be used for vaccine development also for other viruses.