Project Summary The NIAID national protocol intends to enroll at least 1000 COVID19 patients in a study designed to track infected patients through tracking, over time, their immune responses, viral load, and a variety of multi-omic analytes that can provide deep insights into how infection by SARS-CoV-2 is revealed in host defense responses and disease- perturbed networks. At the heart of this study is the establishment of high quality biorepositories that can be used to quantitatively assess viral load, quantitatively interrogate viable PBMCs, and permit direct comparisons between different patients and different time points of disease progression. The nature of the infection, with highly differential patient outcomes, will eventually require significant computational efforts that can account for confounding factors such as co-morbidities, the influence of various therapies that are being broadly tested in these patients, etc. It will also certainly require both broadly available immune characterization tools that can be applied on all patient samples, but also specialized tools that can be used to inform the interpretation of the general analytics. In this project, we propose to integrate two sets of immune cell characterizations into the national NIAID effort. Those characterizations include single cell, functional phenotyping of select immune cell classes via an analysis designed to quantitate the levels of 35 secreted proteins from up to 2000 single cells of a given immune cell type. The second characterization is based upon reducing proteins from the SARS-CoV-2 into peptide antigen-major histocompatibility complex (pMHC) libraries that can be used to identify SARS-CoV- 2 antigen-specific CD8+ and CD4+ T cell populations from isolated, viable PBMCs. These assays provide deep and complementary information that will significantly inform the interpretation of the immune phenotyping assays that constitute the COREs of the NIAID study.