RNA-protein interactions at the host-viral interface of SARS-CoV-2 infections

RNA viruses are a persistent threat to human health and have caused numerous public health emergencies in recent years. In particular zoonoses, the transmission of a virus from animals to humans, have epidemic potential when they are accompanied by the acquisition of human-to-human transmissibility, as it occurred for the recently emerged human coronavirus, SARS-CoV-2. A better understanding of the intricate relationship between host cells and viruses that goes beyond the innate immune response is fundamental to unveil the mechanisms that allow viruses to efficiently co-opt and reprogram cellular machineries for viral replication and adapt to new host species.This proposal will profile RNA-protein interactions at the host-viral interface of SARS-CoV-2 infections with a particular focus on the identification of host RNA-binding proteins (RBPs) that are instrumental for viral replication. Co-option of host RBPs has been demonstrated for a large number of RNA viruses and is essential for the successful completion of the viral life cycle. However, our current knowledge is mostly limited to single case descriptions in humans and lacks a comprehensive characterisation of host RBPs across different species that either promote or inhibit viral replication. In-depth profiling of such host-viral interactions during SARS-CoV-2 infection will give insights into host adaptation and lend a better understanding of the evolutionary consequences that arise from these interactions. In this proposal, we will profile the host-viral interface of SARS-CoV-2 infections by pursuing the following Aims:i) Characterisation of RNA-protein interactions and temporal dynamics of SARS-CoV-2 infection.ii) Functional characterisation of host-viral RNA-protein interactions and evolutionary consequences.iii) Comparative analysis of RNA-binding proteins between host species and impact on viral adaptation.The insights gained from the proposed work are of high relevance, not just during the current COVID-19 pandemic, but present an important foundation to better understand the biology and host adaptation mechanisms of RNA viruses. The proposed work will provide a characterisation of direct RNA-protein interactions during SARS-CoV-2 infection and identify host RBPs with pro- and antiviral properties, alongside their cognate binding sites across the viral genome. Taking the evolutionary consequences into account that arise from these interactions, the proposed work will identify nucleotide sequences within the viral genome that are under evolutionary constraint to maintain host RBP binding and will help to better understand and anticipate viral evolution. Furthermore, the evolutionary comparison of RNA-binding proteins between host species will identify endogenous RBPs acting as species-specific determinants of host range and give insights into how host RBPs influence viral adaptation. The immediate impact of this work lies in the identification of conserved viral sequences that can be used as target sites for RNA-based antiviral strategies and the identification and characterisation of host RBP interactions as potential new drug targets for SARS-CoV-2 infections. Beyond the specific insights that will be gained on the SARS-CoV-2 host-viral interface, this work will have important implications for our understanding of RNA viruses and their adaptation to new host species, with the potential to unveil host RNA-binding proteins as important players in viral host range.