Each point indicates a cell, and blue lines indicate the mean. (A) In the low multiplicity of infection (MOI) experiment, 254 infected cells were identified by single-cell RNA sequencing. Viral transcription was similar in cells that expressed both barcoded viral genes and cells that were missing expression of one or both. Viral genomes in the low MOI experiment were analyzed using long-read viral genome sequencing. In total, 131 infected cells had complete PacBio long-read sequencing data for every expressed viral gene. On average, cells with complete sequencing coverage had higher viral transcription than cells without complete sequencing coverage. Also, 91 infected cells had long-read sequencing of all expressed viral genes and expressed both barcoded viral genes. On average, cells with all measurements had slightly higher viral transcription than cells without all measurements. (B) In the high MOI experiment, 357 infected cells were identified. In total, 290 cells expressed both barcoded genes, providing complete measurements for that sample. Cells with expressing both barcoded genes had higher viral transcription, on average.