A primary nasopharyngeal three-dimensional air-liquid interface cell culture model of the pseudostratified epithelium reveals differential donor- and cell type-specific susceptibility to Epstein-Barr virus infection
Fig 5
Identification of EBV-infected cell types from scRNA-seq performed on a pseudo-ALI culture from donor no. 4.
(A) Uniform Manifold Approximation and Projection (UMAP) plots displaying the major cell clusters and assigned identity from host marker genes. Schematic displays the cell types in the pseudostratified nasal epithelium that are represented in the cell clusters. (B) Comparison of alignment methods against different EBV genome annotations by UMI counts and numbers of cells. (C) The percentage of EBV-infected cells is displayed for each cluster. Shown are the results from alignment to the fused annotation EBV genome, (D) Density plots of log10 transformed pseudocount (UMI count+1) for EBV reads against normalized cell numbers displayed for each cell cluster. Cell numbers are normalized for the total number of cells in each cluster. Cells are grouped by EBVnegative, EBVlow and EBVhigh populations designated by reads aligning to the EBV genome. Density plots with a similar profile are similarly colored. Where applicable (B-C) cells with reads aligning to the EGFP gene is also shown.