Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 disease specific mechanisms and vulnerabilities.

Coronaviruses constitute a constant threat as documented by the recent emergence of SARS-CoV-2 that has caused more than 2,5 million deaths worldwide. Despite this our understanding of coronaviruses and how they interact with their host is very limited. Here we describe a novel phage display library for the discovery of viral short linear interaction motifs (SLiMs) from RNA viruses that mediate binding to human host factors. We utilize this library to uncover the unique patterns of viral SLiMs mediating SARS-CoV-2 - host factor interactions. This established a specific interaction between the human G3BP1/2 proteins and an xFG peptide motif in the viral nucleocapside (N) protein that when disrupted reduce viral replication and infection. We show that the N protein through this xFG motif modulates the G3BP1/2 host interactome by competing with numerous cellular xFG containing proteins and inhibits G3BP1/2 mediated stress granule formation. Collectively our work outlines a strategy for system-wide understanding of viral-host factor interactions that provides both mechanistic insight and pinpoints therapeutically relevant interactions for development of novel antiviral strategies.