Fig. 3: Altered myeloid differentiation and persistent neutrophil accumulation in the SARS2_PASC group, with prolonged presence of S1 antigen.

a UMAP plot showing myeloid cell populations. b Proportions of MQ, monocyte and neutrophil populations across different groups. c Multiplex immunofluorescence image of 30 dpi lung tissues. Each group of tissues was stained with DAPI (nuclei, blue), MPO (green) and CD68 (red) (scale bars, 200 μm). d Quantification of the percentage of MPO⁺ and CD68⁺ cells in 30 dpi lung tissues (n = 3). e Trajectory analysis depicting the differentiation of myeloid progenitor cells into either monocytes/MQ or neutrophils with Monocle3. The UMAP is colored by pseudotime. Arrows 1 and 2 indicate distinct differentiation paths. f, g Feature plots showing CEBPE (f) and IRF8 (g) gene expression in each group, respectively. h Representative images showing IHC results of viral antigens in lung tissue. Arrowheads indicate antigen-positive cells (scale bars, 20 μm). i–k Quantification of the percentage of SARS-CoV-2 (SARS2) S1-positive (i), N-positive (j) and IAV NP-positive (k) cells in lung tissue at different dpi. l Magnified images (scale bars, 20 μm) comparing the presence of antigens and immune cells at 30 dpi. Arrowheads indicate monocytes/MQs, arrows indicate neutrophils and asterisks highlight areas of inflammation. Data are presented as means ± s.d. (d and i–k). Statistical significance is indicated as follows: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, ns (P > 0.05). The P values were estimated using one-way ANOVA. Myeloid_prog, myeloid progenitor cells; CTRL, control group; IAV_rec, IAV_recovery group; SARS2_rec, SARS-CoV-2_recovery group; SARS2_PASC, SARS-CoV-2_non-recovery group; S1, spike protein S1 subunit; N, nucleocapsid; NP, nucleoprotein.