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Systematic Investigation of Host-Pathogen Interactions Identifies Novel Pan-Viral Gene and Drug Targets for Influenza A Viruses and SARS-CoV-2


Influenza A Virus (IAV) is a recurring infectious respiratory virus that causes seasonal infections and global pandemics. With increasing antiviral drug resistance and limited yearly vaccine efficacy, there is a need for new therapeutic treatments. Host-directed therapies offer an alternative treatment strategy, however development of these therapies requires identifying host proteins and signaling pathways that are targeted and rewired by IAV and that are essential for infection. Here, we employed quantitative proteomics, functional genomics and pharmacological screening to systematically identify host factors for three clinical IAV strains (pH1N1, H3N2, H5N1) in three cell types relevant to infection (A549, NHBE, THP-1). We identified 332 IAV-human protein-protein interactions (PPIs) between 214 human proteins and 12 IAV proteins, and 13 IAV-modulated kinase pathways including PRKDC and MAPK signaling. Exome sequencing data of patients with benign or severe influenza disease revealed that predicted loss-of-function genes associated with severe influenza disease are significantly changing in protein abundance (15 proteins) and phosphorylation status (25 proteins and 54 phosphorylation sites) during IAV infection, and include variants mapping back to five PPI factors. This analysis highlighted interferon alpha/beta signaling and TLR signaling as potential molecular drivers of disease severity. Functional genomic screening of our identified PPI and signaling targets uncovered 54 human genes that regulate IAV infection. Given that IAV co-circulates seasonally with severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, we screened these 54 genes against SARS-CoV-2 infection and identified two human genes (COPB1, AHNAK) that act as pro-viral factors for both IAV and SARS-CoV-2 infection. To discover pan-IAV and pan-respiratory virus host-directed therapies, we screened a total of 37 pre-clinical or FDA-approved compounds against pH1N1, H3N2 and H5N1 IAV infection. 16 compounds suppressed replication of at least one IAV strain, with seven compounds showing pan-IAV antiviral activity. Five compounds (Dinaciclib, MAPK13-IN-1, Gilteritinib, Pictilisib, MK-2206) targeting five kinase pathways (CDK2, MAPK13 (p38?), FLT3/AXL, PI3KCA/PI3KCD, pan-AKT) showed antiviral activity against infection by multiple strains of IAV and SARS-CoV-2. These represent putative targets for pan-respiratory virus host-directed therapies.

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