Developing functional genomic tools

Genetic screens have transformed our ability to interrogate cellular factor requirements for viral infections, but most current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information that is often based on survival of infected cells.
By engineering HCMV to express sgRNA libraries directly from the viral genome, we recently tackled these shortcomings and developed a sensitive, versatile, virus-centric approach that allows high-resolution profiling of HCMV propagation (Finkel et al., Nature 2024). In this approach, which we termed VECOS (Virus encoded CRISPR-based direct readOut Screening system), after a virus encoding an sgRNA infects a cell that expresses Cas9, the targeted gene is knocked-out and the level of sgRNAs (which are part of the viral genome) serve as a direct readout for the effect on virus propagation.

Since thousands of viral genome copies are synthesized in every infected cell, this screening approach is extremely sensitive. Furthermore, by probing sgRNA abundance in infected cells, secreted particles and infectious viruses, we can infer which step of infection each perturbation affects, providing a multi-dimensional perspective on viral-host interactions.
We are continually applying this methodology to study different processes, but also adapt it to study different infection models, such as organoids and mice and further, to different viruses.