Fig. 4: Cellular immune response to vaccination and challenge in blood.
a–e, Analysis of cellular composition and gene expression by scRNA-seq at 2 dpc in blood of prime-boost-vaccinated hamsters. a, Manual count of cells per ml blood. b, Frequencies of indicated cell types among blood cells. Dotted lines mark the mean levels found in naïve hamsters (n = 3, naïve hamster data derived and reprocessed from ref. 26). Bar plots with mean ± s.e.m., n = 3. One-way ANOVA and Tukey’s multiple comparisons test were conducted. c, 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 FC and P values, respectively, in vaccinated compared to mock-mock-vaccinated animals. Padj were calculated by DEseq2 using Benjamini–Hochberg corrections of two-sided Wald test P values. Genes are ordered by unsupervised clustering. d, Dot plots showing expression of selected B-cell development marker genes in the blood B-cell subclusters shown in Supplementary Fig. 9a. The size of the dot represents the fraction of cells in which at least one unique molecular identifier (UMI) of the respective gene was detected, while the colour is proportional to the average expression in those cells. e, Frequencies and numbers of pre-plasmablast (pre-PB) identified in B-cell cluster 3 and memory to pre-plasmablast transitioning cells (mem->pre-PB) identified in B-cell cluster 6. Bar plots with mean ± s.e.m., n = 3. One-way ANOVA and Tukey’s multiple comparisons tests were performed; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
