Persistent viral infection in the Drosophila fat body is associated with immune activation at the single cell level

Background Viruses are ubiquitous and can spread in two main ways: vertically, which involves transmission through or associated with gametes, and horizontally, which occurs through direct contact, airborne transmission, or indirect contact, such as through ingestion. Vertically transmitted, low virulence viruses can go undetected by both the immune system and researchers, and cause chronic, asymptomatic infections. In many Drosophila studies, researchers are unaware or ambivalent about the fact that the flies used may be infected with persistent viruses. Although they often have minimal or no observable fitness costs in laboratory fly samples, recent studies suggest that an increase in viral titer is associated with a decrease in lifespan. Results In this study, we explored changes in expression occurring during these cryptic virus infections. To achieve this, we utilized publicly accessible single-nuclear RNA sequencing (snRNA-seq) data of the Drosophila fat body, where we detected persistent infections of Nora and Drosophila A virus. We observed that Nora virus and Drosophila A virus exhibit broad cell-type tropism in the Drosophila fat body, and when coinfected, Drosophila A virus showed higher viral titer and cell infection rate. Transcriptomic analysis revealed substantial immune pathway alterations: Nora virus is broadly associated with upregulation of immune pathways (IMD, Toll), whereas Drosophila A virus is associated with downregulation of specific Toll pathway effector genes. Additionally, the expression of somatic transposable element (TE) transcripts was associated with viral infection, showing mating status-dependent patterns with downregulation in Nora virus-infected virgin flies and upregulation in mated flies for both viruses. Conclusions Overall, our results indicate that cryptic and persistent viral infections in Drosophila elicit transcriptional changes in the fat body, including activation of immune responses, and are associated with dysregulation of TE activity in somatic fat body cells.