Comparative single-cell analysis reveals IFN-g as a driver of respiratory sequelae post COVID-19

Post-acute sequelae of SARS-CoV-2 infection (PASC) represents an urgent public health challenge, with its impact resonating in over 60 million individuals globally. While a growing body of evidence suggests that dysregulated immune reactions may be linked with PASC symptoms, most investigations have primarily centered around blood studies, with few focusing on samples derived from post-COVID affected tissues. Further, clinical studies alone often provide correlative insights rather than causation. Thus, it is essential to compare clinical samples with relevant animal models and conduct functional experiments to truly understand the etiology of PASC. In this study, we have made comprehensive comparisons between bronchoalveolar lavage fluid (BAL) single-cell RNA sequencing (scRNAseq) data derived from clinical PASC samples and the relevant PASC mouse model. This revealed a strong pro-fibrotic monocyte-derived macrophage response in respiratory PASC (R-PASC) in both humans and mice, and abnormal interactions between pulmonary macrophages and respiratory resident T cells. IFN-g emerged as a key node mediating the immune anomalies in R-PASC. Strikingly, neutralizing IFN-g post the resolution of acute infection reduced lung inflammation and tissue fibrotic changes in a mouse model of R-PASC. Our study underscores the importance of performing comparative analysis to understand the root cause of PASC for developing effective therapies. Overall design: To facilitate the single-cell gene expression (GEX), PBMC and BAL cells from donors and MA10 infected mice at indicated time points were harvested and barcoded with 10X 5' Library & Gel Bead Kit v1.1 or 3' Library & Gel Bead Kit v3.1 in a BSL2 lab (human samples) or a ABSL3 lab (animal samples).