Background <p>At the end of 2019, severe acute respiratory syndrome (SARS) caused by the novel coronavirus SARS-CoV-2 emerged in China, representing one of the most significant global health threats of the twenty-first century. This study aimed to evaluate the phenotypic and cellular activation of epithelial cells in tracheal aspirate samples from patients with severe COVID-19.</p> Methods <p>A total of 48 samples were collected from 28 mechanically ventilated patients and analyzed using flow cytometry and conventional microscopy.</p> Results <p>The results revealed a high prevalence of basal, ciliary, undifferentiated cells, and pneumocytes displaying morphological abnormalities. Samples were classified into hypocellular and hypercellular profiles based on total cell counts. These profiles were associated with clinical outcomes, with hypercellular samples more frequently observed in patients who died. Hypercellular samples exhibited increased frequencies of basal, undifferentiated cells and pneumocytes, as well as a greater presence of CD45⁺ cells with elevated HLA-DR expression, indicating an influx of activated leukocytes and antigen-presenting cells. In contrast, hypocellular samples showed a higher proportion of CD45⁻PanCK⁺ cells, reflecting a predominance of epithelial cells. Hypercellular samples also demonstrated increased EpCAM⁺PanCK⁺ epithelial cells with more expression of Spike in the context of intense inflammation. ICAM-1 expression was elevated in CD45⁺ cells from hypercellular samples, while reduced in CD45⁻ cells. Finally, a superior connectivity was found for networks of correlations of hypercellular samples, especially amongst the compartments of cells expressing EpCAM.</p> Conclusion <p>Together, these findings identify two distinct cellular profiles that may serve as prognostic indicators in severe COVID-19.</p>