Fig. 1: 17D infection leads to faster spread and more robust innate immune responses than infection with the virulent strains Asibi or Dakar in Huh7 cells. | Nature Microbiology

Fig. 1: 17D infection leads to faster spread and more robust innate immune responses than infection with the virulent strains Asibi or Dakar in Huh7 cells.

From: Amino acid changes in two viral proteins drive attenuation of the yellow fever 17D vaccine

Fig. 1

a, Intracellular YFV genome copy numbers measured at indicated timepoints by RT–qPCR (MOI = 0.05). Data are mean ± s.d. from 3 experiments with 2 biological samples (n = 6). LOD, limit of detection. b, YFV E antigen-positive cells as measured by flow cytometry at 48 hpi (MOI = 0.05). Data are mean ± s.d. from 3 experiments with 1 or 2 biological samples (n = 5). c, Experimental workflow for bulk RNA-seq on mScarlet-positive cells. Illustration generated with figures from the NIAID NIH BIOART source. d, Number of up- or downregulated DEGs in YFV- vs mock-infected cells. e, Gene set enrichment analysis (GSEA) of 17D-, Asibi- or Dakar-infected cells vs mock-infected cells. Shown are the top-10 hallmark pathways ranked by adjusted P value between 17D- vs mock-infected cells. UPR, unfolded protein response. NES, normalized enrichment score. f, Heat map showing expression (by z-score) of 14 ISGs across experimental replicates of 17D- vs Asibi-infected cells (n = 6). g, Relative expression by RT–qPCR of IFIT2 and IFIT3 in Huh7 cells at 48 hpi with non-reporter 17D, Asibi or Dakar YFV (MOI = 0.5). Data are mean ± s.d. from 3 experiments with 3 biological samples (n = 9) h, Schematics of the YFV genome organization symbolically showing the presence or absence of non-synonymous and synonymous mutations found in 17D vs Asibi. i, Phenotypic comparison of mScarlet reporter viruses corresponding to the genomes shown in h. Frequency of mScarlet-positive cells (MOI = 0.05) by flow cytometry (left), and relative expression of IFIT2 (middle) and IFIT3 (right) by RT–qPCR at 48 hpi (MOI = 0.5). Data are mean ± s.d. from 2 experiments with 3 biological samples (n = 6). Two-way (a) or one-way (b,g,i) analysis of variance (ANOVA) followed by Tukey’s ad hoc test for multiple comparisons. For a, P values are only shown in comparison to 17D at multiple timepoints as indicated by colour. For i, P values are only shown in comparison to Asibi. P values were calculated in GSEA analysis and adjusted using the Benjamini–Hochberg method (e).

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