Sex differences and immune correlates of Long COVID development, persistence, and resolution

Sex differences have been observed in acute coronavirus disease 2019 (COVID-19) and Long Covid (LC) outcomes, with greater disease severity and mortality during acute infection in males and greater proportions of females developing LC. We hypothesized that sex-specific immune dysregulation contributes to LC pathogenesis. To investigate the immunologic underpinnings of LC development and symptom persistence, we performed multi-omic analyses on blood samples obtained during acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and 3 and 12 months post infection in a cohort of 45 patients who either developed LC or recovered. Several sex-specific immune pathways were associated with LC. Males who would later develop LC exhibited increases in transforming growth factor (TGF)-β signaling during acute infection, whereas females who would go on to develop LC had reduced TGFB1 expression. Females who developed LC demonstrated increased expression of XIST, an RNA gene implicated in autoimmunity, during acute infection compared with females who recovered. Many immune features of LC were also conserved across sexes, such as alterations in monocyte phenotype and activation state. Nuclear factor (NF)-κB transcription factors were up-regulated in many cell types at acute and convalescent time points. Those with ongoing LC demonstrated reduced ETS1 expression across lymphocyte subsets and elevated intracellular IL-4 in T cell subsets, suggesting that ETS1 alterations may drive aberrantly elevated Th2-like responses in LC. Altogether, this study describes multiple innate and adaptive immune correlates of LC, some of which differ by sex, and offers insights toward the pursuit of tailored therapeutics. Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from: 45 participants at approximately 3 months post SARS-CoV-2 infection, of whom 36 had developed symptoms consistent with Long COVID and 9 had fully recovered; 23 participants at approximately 12 months post SARS-CoV-2 infection, of whom 12 had persistent Long COVID (at 3- and 12-months post infection) and 11 had fully recovered by 12 months post infection despite having symptoms of Long COVID at 3 months post infection; and 21 participants during acute SARS-CoV-2 infection, of whom 15 would go on to develop Long COVID at 3 months post infection and 6 would go on to fully recover at 3 months post infection. Additionally, PBMCs from 7 other donors (AR#) were included in sublibrary prep but were part of a different experiment.