Host-virus co-expression patterns across viral infection states.

Cells were re-ordered based on their infection index (PC1 from Fig 3C) to reconstruct pseudotemporal separation of the infection process. (A, B) Clustogram representation of the average expression value of viral (A) and host (B) genes across the infection dynamics of CCMP2090 using a sliding window approach (window size = 20 cells). (C) Expression profile of selected host genes along the viral infection index (PC1) in the sliding windows of 20 cells reveals early induction of host genes prior to viral gene expression. Solid line represents the border between uninfected cells and infected cells which were analyzed separately. The dotted line represents the separation between cell expressing viral genes and cells that do not express viral genes in the population of infected culture.