Figure 6.

Spatial whole-transcriptome profiling of the olfactory epithelium in COVID-19

(A) Scanned image of a section through the OM of COVID #8. RNAscope for S was combined with IHC for KRT8/18 and pan-KRT. Four AOIs in the OE are indicated, with a low viral load (13 and 14) or a high viral load (20 and 7). SYTO 83 served as nuclear stain.

(B) Magnification of AOI 13 and AOI 7.

(C) Boxplots of nucleus counts of AOIs with low versus high viral load, with the numbers of the four AOIs shown in (A). NS, not significant.

(D) Boxplots of log₂ normalized expression counts for orf1ab (p = 7.96e-07).

(E) Regression curve between normalized expression counts for S (x axis) and orf1ab (y axis).

(F) Volcano plot with the magnitude expressed as log₂ FC (x axis) and significance expressed as –log₁₀ of the unadjusted p value (y axis) of differential expression of 9,262 genes (dots) in WTA data between the ten ORF1ab High AOIs and the seven ORF1ab Low AOIs. Dashed vertical lines represent a |log₂ FC| of one. Genes of interest are labeled. Dots with gray outlines are the 26 OR genes. Dots with p values with a false discovery rate (FDR) <5% are shown in red.

(G) Log₂ FC values of markers for sustentacular cells (bottom) and OSNs (middle) and of OR genes (top). The asterisk indicates the average of the 26 differentially expressed OR genes.

(H) Boxplots of log₂ normalized expression counts for the 26 differentially expressed OR genes (26 OR) and the 8 OSN markers (OSN).