Single-phage profiling illuminates viral individuality during cell fate determination

The determination of host fate arises through the stochastic transcription from multiple viral genomes present within each cell, but this activity remains hidden from empirical interrogation, which typically stops at the whole-cell level.

Here we use parallel sequential fluorescence in situ hybridization (par-seqFISH), followed by spatial clustering of phage-encoded transcripts within each cell, to profile the transcriptional activity of individual phages during synchronized infection of Escherichia coli (E. coli) by bacteriophage lambda. At the whole-cell level, transcription kinetics capture the developmental choice between lysis and lysogeny, and further demonstrate that viral replication is required for the emergence of diverging fate decisions.