Borna disease virus (BoDV), a single-stranded RNA virus of negative polarity, has puzzled researchers for decades, because of its neurotropism and non-cytolytic multiplication strategy. Its recent recognition as a zoonotic agent causing severe encephalitis and brain dysfunction has provided further impetus for increasing our knowledge on this enigmatic pathogen. To date, very little is known regarding the BoDV replication modalities. It is the only animal Mononegavirales to replicate in the nucleus, where it assembles viral factories that, strikingly, are physically bound to the neuronal chromatin. The only available structural information is the X-ray structure of the RNA-free nucleoprotein and nothing is known regarding its recognition of the genomic RNA or the organization of its nucleocapsid. Intriguingly, sequence analysis predicts that the BoDV polymerase is radically different from that of other Mononegavirales, being 20 % shorter and not containing the canonical RNA-capping motifs. In particular, the methyltransferase domain seems absent, strongly suggesting the recruitment of specialized host factors at viral factories -such as the capping machinery- to complement this activity which is essential for the maturation of viral mRNAs. Finally, the functional consequences of the binding of viral factories onto the chromatin, notably its impact of neuronal epigenetics and neuronal communication, are also completely unexplored. In this context, the Bavarian project aims at providing an integrative and multiscale vision of the BoDV replication complex. Our multi-pronged proposal will describe the structural organization and explore the BoDV replication complex modus operandi within infected cells. To tackle these questions, our three teams will combine their expertise, implementing cutting-edge structural biology, biochemistry, virology and neuronal functional assays. Our complementary approaches will allow a fine characterization of: (i) the architecture of the BoDV replicative machinery, (ii) its viral-host polypeptides interplays and (iii) the impact of altering the viral replication on viral fitness, neuronal epigenetics and function. Our project will provide an unmatched deciphering of BoDV pathogenic mechanisms and, in a broader view, will represent a breakthrough in the field of RNA virus family evolutionary mechanisms. Indeed, Bavarian will focus on the only non-retroviral RNA virus known so far that needs to interact with the host DNA genome to persist and proliferate. To achieve its goals, our project groups three teams with complementary expertise. The team of the coordinator (IBS, Grenoble) is composed of biochemists and structural virologists, with recognized experience in viral replication. Partner-2 (Infinity, Toulouse) has a long-standing expertise in the analysis of the mechanisms and consequences of viral persistence, in particular BoDV, in the central nervous system. Partner-3 (Prism, Lille) has a strong background in proximal interactomics (notably BioID) and systems biology, illustrated by his recent description of whole proteome proximal interactomes of emerging viruses such as Zika and SARS-CoV-2. These recent months, the three teams have established a very efficient collaboration, which has led to a very convincing set of preliminary data that strongly ensures the chances of success of the proposed program. The recent SARS-CoV-2 pandemic is a vivid reminder that no pathogen should be under-estimated. Indeed, deciphering the interaction of viruses with target cells is essential to gather clues for therapeutic intervention. Notably, increasing our knowledge on the organization of viral replication complexes is instrumental, because it often allows to identify strategies to block not only one, but often several viruses. Obtaining original data on the unexplored BoDV system could therefore open the road for finding new antivirals and/or therapeutic strategies, which may be applicable to many pathogens.