Virus-host protein co-expression networks reveal temporal organization and strategies of viral infection

Viral replication is a complex dynamical process involving the global remodeling of the host cellular machinery across several stages. In this study, we provide a unified view of the virus-host interaction at the proteome level reconstructing protein co-expression networks from quantitative temporal data of four large DNA viruses. We take advantage of a formal framework, the theory of competing networks, to describe the viral infection as a dynamical system taking place on a network of networks where perturbations induced by viral proteins spread to hijack the host proteome for the virus benefit. Our methodology demonstrates how the viral replication cycle can be effectively examined as a complex interaction between protein networks, providing useful insights into the viral and host’s temporal organization and strategies, key protein nodes targeted by the virus and dynamical bottlenecks during the course of the infection. [Display omitted] •Virus-host co-expression networks are reconstructed from temporal proteomics data•Viral replication cycles are dynamically organized on a network of networks•The theory of competing networks unveils viral infection complex dynamics•Network structure and node importance reveal biological functionality Molecular network; Virology; Proteomics