Fig. 3: Characterisation of individual nasal cell transcriptional responses to SARS-CoV-2.

Nasal ALI cultures were infected with SARS-CoV-2 (MOI 0.1). At 24 h post-infection (hpi), cell suspensions were prepared from two representative donors for single-cell RNA sequencing (scRNA-seq) and 28,346 individual transcriptomes passing quality control (QC) were analysed. a Violin plot representing the composite interferon-stimulated gene (ISG) signature score that was defined based on a published nasal cell dataset from cells treated with IFN alpha and IFN gamma. Gene set scores greater than zero suggest expression levels higher than background gene expression. The bottom and the top of the boxes correspond to the 25th (Q1) and 75th (Q3) percentiles, and the internal band is the 50th percentile (median). The plot whiskers represent the 95% confidence intervals show down to the minimum (Q1−1.5*IQR) and up to the maximum (Q3 + 1.5*IQR) value. IQR = interquartile range. Outside points correspond to potential outliers. See Supplementary data 6 for exact values. Two-sided Wilcoxon rank sum testing was performed for each cell type vs all with Benjamini–Hochberg correction (***P < 0.0008, ****P < 0.0001). b Differential expression (DE) analysis by Wilcoxon rank sum test was undertaken to compare mock-infected cell transcriptomes with those from bystander cells (without detectable viral transcripts) and infected cells (with detectable viral transcripts) from the virus-exposed cultures. Volcano plots were generated with vertical lines marking ±1.5 fold change cut-offs (note log₂ scale) and the horizontal line marking an adjusted P value cut-off of 0.05 (<0.05 was considered statistically significant). Individual genes coloured as non-significant (light blue) and significant (red). Labels indicate viral transcripts (dark blue) and epithelial-cell specific ISGs (black). c Gene-set enrichment analysis was undertaken by ordering genes by fold change difference between mock-infected and infected cells by cluster (two-sided Wilcoxon rank sum statistical test with Bonferroni multiple testing correction). Vertical lines indicated adjusted P value cut-off of 0.05. NES = normalised enrichment score, MOI = multiplicity of infection.