Traitor-virus-guided discovery of antiviral factors

Viruses may seem smart since they rapidly develop new skills to spread in humans. However, they are actually just masters of trial and error. Their short generation time, enormous reproduction and high variability allows viruses to try countless variations. A few of these will enhance viral spread and, in the worst case, enable viral pandemics. It is conceivable that viruses evolve to counteract those defence mechanisms that would otherwise be most effective against them. Usually, it is hard to assess why specific changes are advantageous. This is especially true for adaptations enabling viral pathogens to counteract innate antiviral factors because these cellular proteins and their viral antagonists are numerous and highly versatile. Here, I propose to combine the advantages of the revolutionary CRISPR/Cas9 technology with the enormous adaptive power of viruses to develop a novel approach allowing robust, specific and genome-wide unmasking of antiviral mechanisms. In principle, we will equip HIV-1 with genetic scissors to convert them into traitor viruses revealing their cellular opponents. To achieve this, we will generate libraries of replication-competent HIV-1 constructs expressing guide RNAs as genetic tools with the potential to inactivate every human gene in Cas9 expressing cells. Virus variants expressing guide RNAs eliminating antiviral genes will be selected by in vitro passaging and identified by next generation sequencing. Utilization of different viral backbones will allow the discovery of key defence factors against viral zoonoses and spread in humans. Finally, we will determine the antiviral spectrum and inducibility of innate antiviral factors to identify vulnerabilities of viral pathogens that can be exploited in preventive and therapeutic approaches. The project will establish and apply an innovative, highly versatile approach to uncover our antiviral defence mechanisms with the ultimate goal is to achieve better control of viral pathogens.