Bacteriophage self-counting in the presence of viral replication

Significance Viral dormancy, in which the infected cell is not killed but rather becomes the long-term residence of the parasite, is a hallmark of viruses across kingdoms from bacteriophages to HIV. When and how viruses decide to opt for this lifestyle remains mysterious. Phage lambda, which serves as a paradigm for viral dormancy, is reported to count the number of coinfecting viruses and then uses this value to assess the abundance of potential hosts and decide whether to become dormant. Here, we use a single-cell measurement of viruses and messenger RNA together with mathematical modeling to illuminate how lambda performs this task. When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda’s decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision—lysis upon single-phage infection and lysogeny at higher MOI.