Infectious respiratory diseases comprise the 4th most fatal group of diseases worldwide. Most studies on COVID-19 lack appropriate comparison to other viral pneumonias with similar severity. Here, we leverage the SCRIPT cohort at NWU Chicago for longitudinal proteomic profiling of bronchoalveolar lavage fluid (BALF) and patient plasma to analyze pathogen-specific differences during disease progression. We used mass spectrometry to analyze BALF and matched plasma from COVID-19 (n=14), bacterial pneumonia (n=8), influenza (n=8) patients, and non-pneumonia controls (n=8) at up to five time points after intubation in the intensive care unit.

BALF of COVID-19 patients was specifically enriched in immunoglobulins, blood clotting proteins, and collagens, suggesting increased fibrogenesis and B-cell immunity already at the time of intubation compared to other bacterial or viral types of pneumonia. We employed our recently developed Differential Antigen Capture assay to analyze the binding specificities of plasma antibodies in all patients and identified potential autoantibody responses in COVID-19. Bacterial pneumonia was rich in neutrophil degranulation proteins, whereas influenza samples contained high levels of mucins. Computational deconvolution of the proteomics samples using scRNA-seq-derived marker gene sets predicted increased plasma cell and myofibroblast frequency in COVID-19, and neutrophilia in bacterial pneumonia. Importantly, the differential signatures in BALF were partially conserved in patient plasma.

In summary, we identified specific proteomic signatures of COVID-19 compared to influenza and bacteria-driven pneumonia, suggesting increased early onset local B-cell immunity and fibrogenesis in COVID-19.