Sex, obesity, immunometabolism, and viral persistence in post-acute sequelae of SARS-CoV-2 infection

Summary After SARS-CoV-2 infection, a significant percentage of people develop persistent symptoms or health complications, often referred to as 'long COVID' or post-acute sequelae of COVID-19 (PASC). The host, virus and environmental factors affecting the development of PASC are not well known, which hinders development of therapeutics for patients. There also are no biomarkers for PASC, which complicates development of diagnostics. In the proposed work, we will build on preliminary data showing immune and metabolic dysregulation correlating with specific symptoms of PASC. We have assembled a cross-disciplinary collaborative team with global expertise in SARS-CoV-2 virology, viral immunity, RNA virus persistence, cutting edge tissue-based viral assays, animal models of COVID-19, cohort methodology, infectious diseases diagnostics, high-dimensional single cell data analysis, and sex-based differences in respiratory viral infection. Our team includes the primary investigators of an NIH-funded COVID-19 Serology Center of Excellence and four large COVID-19 clinical studies with > 1500 enrolled participants and longitudinal blood and respiratory mucosal sampling coupled with symptom surveys from 2 days after symptom onset through 18 months after symptom onset. We will study the intersection of persistent viral antigen or RNA, host immune response, sex, obesity, and PASC. Our central hypothesis is that distinct and persistent immune metabolic profiles are associated with specific post-COVID conditions. In Aim 1, we will use immune-metabolic high-dimensional flow cytometry, targeted metabolic gene expression profiling and functional assays, and single cell RNA sequencing to dissect the metabolic and immune programs driving differentiation and function of these unique populations in longitudinal samples from individuals with distinct PASC symptoms and sequelae and those with complete recovery from COVID-19. In Aim 2, we will determine whether specific symptoms and sequelae of PASC are associated with prolonged evolution of SARS-CoV-2-specific B and T cell responses suggestive of viral antigen or RNA persistence and facilitated by obesity. In Aim 3, we will use our novel mouse model of SARS-CoV-2 to evaluate sex differences in the persistence of SARS-CoV-2 RNA or antigen in multiple organs, which may lead to immune-metabolic dysregulation in tissues and correlate with behavioral signs of PASC in mice. Through the experiments outlined in this proposal, we will address whether some form of SARS-CoV-2 persistence contributes to PASC or if PASC is entirely a consequence of a remote virus infection, a question with enormous clinical implications.