Deciphering viral action on host genome structure: a computational physics perspective

Recent experimental findings indicate that several viruses are able to substantially re-organize the host cell genome architecture. Since chromatin three-dimensional (3D) organization is tightly linked to vital cellular functions, investigating how viral infections impact physical mechanisms shaping DNA folding provides useful clues about virus action on gene regulation and consequent activation. This review provides an overview of recent advances in the development of computational modelling approaches used to shed light on how host cell chromatin 3D structure is altered following viral infections, including SARS-CoV-2 and avian influenza IAV-H5N1. Given the flexibility of this approach, such models can be adapted to a wide range of pathogens, making them valuable methods for investigating the specificity of distinct infection mechanisms. Overall, we show how such models can be helpful tools that, in tandem with traditional experimental methods, allow to decipher complexity of infection mechanisms at molecular level from a new perspective.