Leveraging virus-specific T cells as antigen biosensors to interrogate the pathogenesis of long COVID 3632

Abstract Description Millions of people have experienced persisting symptoms for months after SARS-CoV-2 infection, known as long COVID (LC). No proven therapies exist to treat LC, and the mechanisms driving disease remain poorly understood. Persistence of SARS-CoV-2 and reactivation of herpesviruses such as EBV and VZV have been linked to the development of LC, leading us to hypothesize that antigens from these viruses could drive chronic immune stimulation. To track antigen sensing by virus-specific CD4 and CD8 T cells, we analyzed hundreds of human blood samples from LC patients and recovered controls using 35-color flow cytometric assays with multiplexed HLA/peptide tetramers for 53 unique peptides from EBV, CMV, VZV, Flu, and SARS-CoV-2. We observed elevated activation of SARS-CoV-2-, EBV-, or VZV-specific T cells in 40% of LC patients, providing one of the most sensitive measures of immunopathology in LC to date. We also observed that EBV- and VZV-specific T cell activation is frequently triggered during acute SARS-CoV-2 infection. We then sorted thousands of virus-specific T cells from each of over 50 samples using barcoded HLA/peptide tetramers and performed single-cell RNA and TCR sequencing to interrogate the activation state, tissue-specific trafficking signatures, and features of T cell exhaustion in CD4 and CD8 T cells specific for dozens of viral antigens. These data identify distinct immunological signatures in different LC patients and highlight the need for targeted therapeutics. Funding Sources Supported by NIH F32AI181343 and U19AI082630 and the Polybio Research Foundation. Topic Categories Immune Mechanisms of Human Disease (HUM)