Determining the impact of microbial dysbiosis on immune and barrier function in long COVID 2304111

Abstract

Over 11 million people in the US are affected by long-COVID syndrome, or post-acute sequelae of SARS-CoV-2 infection (PASC), occurring in 10% of those infected. Despite advances, PASC studies remain largely observational due to the lack of a good animal model and the disease’s heterogeneity. It is therefore imperative to discover the underlying causes of PASC and develop effective treatments. Recent studies showed that SARS-CoV-2 Spike RNA can persist in the colon for>2 years after infection. Given the frequency of microbial dysbiosis and T cell hyperactivation in PASC, we reasoned that a gut viral reservoir may cause T cell dysfunction by altering the microbial metabolome. To investigate viral persistence, we acquired colon biopsy patients from the University of Chicago colonoscopy clinic and conducted RNAscope targeting SARS-CoV-2 Orf1ab RNA. On the same patient’s stool, we did metabolomic and metagenomic analysis to investigate differences in metabolites from PASC patients. Subsequently, we probed how exposure to PASC metabolites affected T cell activation and metabolism by conducting flow cytometry experiments on T cells exposed to autologous or long COVID metabolites. Using colon biopsy samples from colonoscopy patients, we found evidence of SARS-CoV-2 Orf1ab RNA persistence in patients with persistent symptoms after COVID-19. We also found PASC patient stool was enriched in pro-inflammatory tryptophan metabolites. After TCR stimulation, T cells exposed to long COVID metabolites upregulated the inhibitory marker PD1 while increasing fatty acid synthesis/OXPHOS and reducing fatty acid oxidation, demonstrating that long COVID metabolites reduced the ability of T cells to activate metabolic programs leading to functional impairment. Taken together, our data show that viral persistence may be a frequent occurrence linked to long COVID symptoms and may play a role in promoting a dysregulated inflammatory state by altering the metabolite microenvironment of the gut. Center for Intestinal Inflammatory Diseases (C-IID) P30 DK042086 Mucosal and Regional Immunology (MUC)