Extended Data Fig. 4: Viral gene expression profiles along the productive and abortive trajectory of infection.

a, Gene expression profiles for robustly detected viral genes along the dominant trajectory (clusters ‘infected 1–6’). Cells were grouped in bins spanning 2% of viral RNA and the gene expression (scaled UMIs per gene per cell) averaged for all cells in each bin. The heatmap shows the expression relative to the highest bin. Individual viral genes are ordered by similarity of the profiles, and annotated by genome position, phenotype of cutting within the body of a gene in the pooled virus-directed CRISPR screen (see Fig. 1 and Supplementary Fig. 1), and by the temporal profile as determined in a bulk proteomics study⁵. Note the relationship between a gene’s temporal class and its phenotype in the pooled screen: True-late and leaky-late genes predominantly showed protective phenotypes, whereas earlier classes also contained sensitizing genes. b, Gene expression profiles of viral genes along the abortive trajectory (clusters ‘infected 1–2’ and ‘infected abortive’). Cells were grouped in bins spanning 10% of viral RNA and the gene expression averaged for all cells in each bin. The heatmap shows the expression relative to the expression in an equivalent bin of the dominant trajectory.