Viruses infecting marine phytoplankton drive phytoplankton diversity, terminate blooms and shuttle genetic material. Assessments of the scale of viral impacts on trophic networks are, however, speculative. We investigated fluxes of DNA between host and virus during infection of the prasinophyte alga Micromonas pusilla by phycodnavirus MpV SP1. Under a light–dark regimen, viral genomes accumulated to a transient peak within 24 h, at the expense of both host DNA synthesis and nuclear DNA. Viral genome abundance then declined soon after host lysis. This release of a phosphate-rich nucleotide pool during viral infection of phytoplankton should be considered in trophic models. Lysis required light and was stalled in darkness, meanwhile viral genome replication proceeded slowly in the dark. Viral exploitation of this host is therefore only partially light-dependent and infected phytoplankton are poised to lyse at dawn or if mixed to the photic zone. The chloroplast genome remained intact until lysis, indicating that either this DNA pool is inaccessible or the virus spares the chloroplast for its energy and reductant generation. The photochemical turnover of residual Photosystem II complexes accelerated during lysis, indicating that events in late infection heighten demands on the remaining host photosynthetic systems, consistent with the light dependency of lysis.