PROJECT 2: Determine clinically relevant host-viral dependency networks for respiratory infections including SARS-CoV-2

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PROJECT 2: DETERMINE CLINICALLY RELEVANT HOST-VIRAL DEPENDENCY NETWORKS FOR RESPIRATORY INFECTIONS INCLUDING SARS-COV-2 SUMMARY Respiratory viral infections caused by SARS-CoV-2, influenza A and B viruses, respiratory syncytial virus, and human parainfluenza virus are a significant public health burden globally. Although vaccines are available for some of these viruses, the inequality in access and the constant virus evolution diminish their efficacy. Moreover, effective therapeutics preventing and treating severe respiratory viral diseases are still largely lacking. In Project 2, we will exploit viral dependencies on host factor networks to gain insight into disease mechanisms and develop new therapeutic approaches. We focus on relevant primary cell models, panviral mechanisms and innovative reverse genetics technologies. In Aim 1, proteomics and transcriptomics analyses will be performed with the Technology Core to determine global changes in protein abundance, post-translational modifications, and gene expression profiles in infected primary human lung cells and three-dimensional human airway organoids. Results will be integrated by the Data Management and Bioinformatics and Modeling Cores using existing -omics and human GWAS datasets to search for signatures that correlate with clinical pathogenesis. In Aim 2, virus and host genetics will be used to uncover host dependency factors critical for respiratory infection, using rapid SARS- CoV-2 cloning as well as genome-wide CRISPR-screens. In Aim 3, using supernatants of infected cells and patient serum samples, we will characterize the pro-inflammatory effects of SARS-CoV-2 ORF8 and other secreted viral proteins in correlation with clinical data. With Project 1, we will test their effect on other respiratory viruses and Mycobacterium tuberculosis infection. We anticipate that these studies will have a significant impact on public health measures against respiratory virus infections in the future.