Site Specific Immunophenotyping Assays of COVID19 Patients to Align with NIAID National Study

The NIAID national protocol intends to enroll at least 1000 COVID19 patients in a study designed to track infectedpatients through tracking, over time, their immune responses, viral load, and a variety of multi-omic analytes thatcan 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 beused to quantitatively assess viral load, quantitatively interrogate viable PBMCs, and permit direct comparisonsbetween different patients and different time points of disease progression. The nature of the infection, withhighly differential patient outcomes, will eventually require significant computational efforts that can account forconfounding factors such as co-morbidities, the influence of various therapies that are being broadly tested inthese patients, etc. It will also certainly require both broadly available immune characterization tools that can beapplied on all patient samples, but also specialized tools that can be used to inform the interpretation of thegeneral analytics. In this project, we propose to integrate two sets of immune cell characterizations into thenational NIAID effort. Those characterizations include single cell, functional phenotyping of select immune cellclasses via an analysis designed to quantitate the levels of 35 secreted proteins from up to 2000 single cells ofa given immune cell type. The second characterization is based upon reducing proteins from the SARS-CoV-2into 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 deepand complementary information that will significantly inform the interpretation of the immune phenotyping assaysthat constitute the COREs of the NIAID study.