Fig. 5: Enrichment of Trem2⁺ and Fbp1⁺ macrophages in the lung after SARS-CoV-2 clearance.

a Cell fate inference analysis by CellRank based on monocyte/macrophage scRNA-seq data at d7 and d14. b Boxplot showing the proportion of Trem2⁺ AMs, Fbp1⁺ AMs and proliferating Fbp1⁺ AMs in total Stereo-seq bin80-bins of nine lung slides at each timepoint. Data are represented as mean ± SEM (n = 9 slides per timepoint). Center line, median; box bounds, first and third quartiles; whiskers, 1.5 times the interquartile range. Kruskal–Wallis test. c RNA velocity analysis of AM subpopulations. Arrows indicate the potential directions of state transitions. d Boxplot showing the spatial correlation between different cell types and Fbp1⁺ AMs of nine lung slides at d14. Data are represented as mean ± SEM (n = 9 slides per timepoint). Center line, median; box bounds, first and third quartiles; whiskers, 1.5 times the interquartile range. Kruskal–Wallis test was performed to calculate the P value across different groups. Pearson correlation was performed to calculate the P value of all spots within each slide. Black dots: P < 0.05; gray dots: P ≥ 0.05. Red dotted line represents the correlation value of 0. e, f Representative images of the lung sections of hACE2 mice before and after SARS-CoV-2 infection detected by immunofluorescent staining. TREM2 and CD68 at d0 and d14 (e); FBP1 and CD68 at d0 and d14 (f). TREM2⁺ or FBP1⁺ macrophages were indicated by arrows. Scale bars, 50 μm. g Boxplot showing the proportion of SLAMF9⁺SPP1⁺, TREM2⁺, FBP1⁺, FBP1⁺MKI67⁺, and MARCO⁺CD36⁺TREM2^–FBP1^– macrophages in CD68⁺ macrophages in scRNA-seq data of human lung autopsy samples of control (n = 8) and COVID-19 patients (n = 5). Center line, median; box bounds, first and third quartiles; whiskers, 1.5 times the interquartile range. Data are represented as mean ± SEM. Two-sided Wilcoxon test.