A multidisciplinary approach to identify vulnerabilities of SARS-CoV-2 for vaccine development

The newly discovered coronavirus (CoV) SARS-CoV-2 is responsible for the recent pandemic outbreak of pneumonia that threatens countless lives across the globe. Like all viruses it critically relies on the reprogramming of the cellular metabolism and 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. This will be crucial to design attenuated viruses that can be used as vaccines not only 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 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. Finally, we will apply the knowledge gained to develop synthetic attenuated viruses lacking RNA modifications or containing sequence elements that are difficult to translate during an infection. We will test select viruses by ribosome profiling and in infection experiments. By combining these approaches, we will identify how SARS-CoV-2 interacts with its host and in particular its translation and RNA modification machineries. This will identify drug targets & strategies to rationally design attenuated viruses that can be used for vaccine development.This proposal assembles an interdisciplinary team by joining the forces of three labs that combine expertise in diverse areas like molecular virology of coronaviruses, translation mechanisms (including that of viral RNAs) and of RNA modifications. Importantly, this will allow us to go beyond the current state of the art. In particular since this team has direct access to live virus samples and the ability to create recombinant SARS-CoV-2 for experimentation. We are confident that the combined knowledge generated on this new virus can rapidly facilitate vaccine development.Importantly, we will make our initial ribosome profiling data available immediately after its acquisition to speed up research during this ongoing crisis.