The prevalence of pathogens in wild populations has often been estimated by the appearance of overt symptoms in the host, and this is typically used as the sole gauge of the impact of the pathogen on host dynamics. However, the development of molecular methods has increased the sensitivity with which we can detect asymptomatic infections. Baculoviruses are insect pathogens that, like many microparasites, are usually only found when their hosts reach outbreak densities, when a disease epizootic occurs. Conventional wisdom is that the long-term persistence of baculoviruses relies on their survival in the external environment in the form of occlusion bodies. These are proteinaceous matrices in which the virus particles are embedded, and which provide a degree of protection from UV irradiation. However, Mamestra brassicae has also been shown to harbour a persistent, non-lethal baculovirus infection (M. brassicae nucleopolyhedrovirus) in laboratory culture, which may represent another putative persistence mechanism. Here, we present evidence that such covert infections are also present and frequent in natural populations of the moth. The persistent infections were triggered into the lethal overt state by exposure to another baculovirus, and two closely related but different baculoviruses were subsequently identified as persistent infections within the populations sampled. These results have broad-ranging implications for our understanding of host pathogen interactions in the field, in the use of pathogens as biocontrol agents, and in the evolution of virulence.