Temporal single-cell profiling of bronchoalveolar lavage samples identifies early predictors of fibroproliferative outcomes in SARS-CoV-2 ARDS

During the COVID-19 pandemic, approximately 40% of intensive care unit (ICU) patients developed acute respiratory distress syndrome (ARDS), necessitating mechanical ventilation. ARDS frequently progresses to fibroproliferative lung injury. Clinical observations indicate that once patients enter the fibroproliferative stage of ARDS, there is a narrow window of only a few days in which the condition either begins to resolve or advances toward pulmonary fibrosis, a state associated with increased mortality and long-term functional decline. The transcriptomic mechanisms determining these diverging trajectories, resolution versus progression of fibroproliferation, remain poorly understood. To address this gap, we collected 51 bronchoalveolar lavage (BAL) samples from 34 critically ill SARS-CoV-2 patients at multiple time points, alongside detailed clinical data. Using longitudinal lung tidal volume data from n=1561 COVID-19 patients, we applied dynamic time warping–based clustering to stratify patients into two groups that reflect the distinct disease courses. Subsequently, we performed single-cell RNA sequencing (scRNA-seq) on 209,156 BAL-derived immune cells to investigate cellular and molecular differences between resolution and progression groups. In samples obtained within the first ten days after ICU admission, we detected a pronounced difference in the inflammatory response: patients following the resolution trajectory showed an early and marked upregulation of immune activity. This suggests that molecular signatures of divergent outcomes emerge well before they become clinically apparent. At later stages, more than 30 days after ICU admission, we observed clear evidence of fibroproliferation in the progressive trajectory, including signs of epithelial-to-mesenchymal transition and enhanced CSF1–CSF1R signaling within monocyte-derived macrophages. In contrast, resolution patients displayed a shift from monocyte-derived macrophages toward a restoration of tissue-resident alveolar macrophages, highlighting a cellular reconstitution associated with recovery. Importantly, both the methodological framework and these findings may also be relevant for understanding mechanisms in interstitial lung diseases (ILDs). Publication History Article published online: 04 March 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany