Fig. 2. SARS-CoV-2 infection causes abnormalities in the gut epithelium of mice.

K18-hACE2 were inoculated intranasally with 10⁴ PFU SARS-CoV-2 or mock treatment. a Representative H&E-stained section of the ileum depicting crypt-villus axes from mice at the end of the experiment. Green arrows indicate goblet cells, scale bars correspond to 25 μm. Bottom panels show high magnification images of the indicated crypt with black arrowheads pointing at Paneth cells, scale bars correspond to 10 μm. b Representative anti-lysozyme immunofluorescence images of the ileal crypt (two images per group). White and orange dotted circles delineate normal and abnormal Paneth cells, respectively. Abnormality is characterized by distorted, depleted, or diffuse lysozyme distribution patterns in Paneth cells. Lysozyme = red, DAPI = blue, scale bars correspond to 10 μm. c Quantification of goblet cell number per villus (left), Paneth cells per crypt (middle left) and ratio of goblet cell number / Paneth cell number (middle right) based on H&E staining, and frequency of normal versus abnormal Paneth cell lysozyme distribution pattern based on the immunofluorescence staining as depicted in b (right). Dots represent the mean cell number per crypt-villus unit in each mouse, 50 units were counted per mouse. Results were pooled from three independent experiments with n = 3–5 mice per group for each experiment (n = 8–14 control mice, 12–14 infected mice). Some mice were excluded from the analysis when quality of the slides was too poor. Boxplots indicate median and interquartile ranges (ns = non-significant, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001 two-sided Mann-Whitney U test). d Correlation of Goblet cell number per villus (left, two-sided Pearson correlation r = −0.48, p = 0.015), Paneth cells per crypt (middle, r = 0.14, p value = 0.483) and frequency of abnormal Paneth cell lysozyme distribution pattern (right, r = −0.5528, p = 0.014) for the mice shown in c with α-diversity (inverse Simpson) of the gut microbiome measured at the last day before sacrifice. e Correlation of Goblet cell number per villus (left, r = 0.63, p < 0.001), Paneth cells per crypt (middle, r = −0.29, p = 0.149) and frequency of abnormal Paneth cell lysozyme distribution pattern (right, r = 0.65, p value = 0.003) for the mice shown in c with log₁₀-relative abundances of Akkermansia in fecal samples from the last day before sacrifice; lines: univariate linear regression, shaded region: 95% CI.