COVID Immunophenotyping Study

This application is being submitted to PA-20-135 in accordance with NOT-AI-20-034. We are requesting anemergency supplement to R01AI32774 "Mechanisms of IL-6 mediated T cell pathogenesis in autoimmunity"(PI: Jane H. Buckner). This supplement will directly address the NOT-AI-20-034 research area of interest"Identification and evaluation of the innate, cellular and humoral immune response to SARS-CoV-2infection.....". Importantly, the proposed work is part of the NIAID Immunophenotyping assessment in aCOVID-19 Cohort (IMPACC) study tasked with performing longitudinal immunophenotyping from 1,000subjects with COVID-19. For each subject, among other assays, transcriptomic profiling will be done onperipheral blood, nasal swabs and endotracheal aspirates at six different time points. Specific to theemergency supplement requested here, we will be responsible for performing both the bulk host mRNA-sequencing (RNA-seq) and PCR quantification of viral nucleic acid from SARS-CoV-2 for each of the ~6,000anticipated nasal swab samples. In addition, we will perform a pilot study on 60 nasal swab samplesassessing the potential utility of metagenomic sequencing on these samples to consider it in a larger scale inthis cohort. All work will be done in close coordination with NIAID, University of California, San Francisco(endotracheal RNA-seq), Emory University (blood RNA-seq), and Icahn School of Medicine at Mount Sinai(virology) core sites.