Fig. 2: Pneumonia and pro-inflammatory transcriptional response are strongly reduced in vaccinated animals.
a, H&E-stained lung sections at 5 dpc from the prime-boost vaccination experiment identified perivascular lymphocytes (1), perivascular oedema (2), metaplastic epithelial remodelling (3), endothelialitis (4) and alveolar oedema (5) as labeled by numbered arrows, groups as indicated. Scale bar, 90 µm. b, Two-dimensional projections of single-cell transcriptomes using uniform manifold approximation projection (UMAP) of lung cells (prime-boost experiment). Cells are coloured by cell type as annotated on the basis of known marker genes. c,d, Manual cell count of isolated lung cells per lung lobe (ct cells), calculated numbers of indicated cell types (PMN, monocytic macrophages) based on scRNA-seq-determined cell frequencies for the prime-boost experiment (c) and prime experiment (d). Bar plots with mean ± s.e.m., symbols represent individual hamsters (nsCPD9 = 4, nmRNA = 4, nAd2 = 4, nmock = 4, nsCPD9+sCPD9 = 3, nmRNA+sCPD9 = 3, nmRNA+mRNA = 3, nAd2+Ad2 = 3, nmock+mock = 4), ordinary one-way ANOVA and Tukey’s multiple comparisons test, **P < 0.01. e, Dot plots showing fold changes of gene expression in indicated cell types of the four prime-boost vaccination strategies compared to mock-mock-vaccinated animals. Selected interferon-stimulated genes and pro-inflammatory cytokines are visualized as follows: coloration and point size indicate log2-transformed fold changes (FC) and P values, respectively, in vaccinated compared to mock-mock-vaccinated animals. Adjusted P values (Padj) were calculated by DEseq2 using Benjamini–Hochberg corrections of two-sided Wald test P values. Genes are ordered by unsupervised clustering. f, Localization of viral RNA by in situ hybridization in a longitudinal section of a bronchus at 2 dpc. Red signals, viral RNA; blue, hemalum counterstain. Scale bar, 30 µm.
