Borna disease virus (BDV) infection produces a variety of clinical diseases, from behavioral illnesses to classical fatal encephalitis (i.e., Borna disease [BD]). Since the genomes of most BDV isolates differ by less than 5%, host factors are believed responsible for much of the reported variability in disease expression. The contribution of BDV genomic differences to variation in BD expression is largely unexplored. Here we compared the clinical outcomes of rats infected with one of two related BDV variants, CRP3 or CRNP5. Compared to rats inoculated with CRP3, adult and newborn Lewis rats inoculated with CRNP5 had more severe and rapidly fatal neurological disease, with increased damage to the hippocampal pyramidal neurons and rapid infection of brain stem neurons. To identify possible virus-specific contributions to the observed variability in disease outcome, the genomes of CRP3 and CRNP5 were sequenced. Compared to CRP3, there were four nucleotide changes in the CRNP5 variant, two each in the G protein and in the L polymerase, resulting in four amino acid changes. These results suggest that small numbers of genomic differences between BDV variants in the G protein and/or L polymerase can contribute to the variability in BD outcomes.Borna disease virus (BDV) is a nonsegmented negativestrand RNA virus (6) belonging to the family Bornaviridae (13,46). BDV infection in experimental animals has been used to study the pathogenesis of virus-induced central nervous system damage and as a model for specific human diseases, e.g., autism (37). BDV encodes at least six open reading frames (ORFs) in three transcription units: nucleoprotein p40 (N), p10 (X), phosphoprotein p24 (P), matrix protein gp18 (M), membrane glycoprotein gp94 (G), and an RNA-dependent RNA polymerase p190 (L polymerase) (6, 13, 57). Virus replication and transcription take place in the nucleus, a characteristic of Bornaviridae that is unique in the order Mononegavirales (5,8,12,13,46). BDV naturally infects a wide range of warm-blooded hosts (41). In horses and sheep, BDV causes classical Borna disease (BD), a fatal mononuclear inflammatory encephalomyelitis with severe signs of neurological disease (as reviewed in reference 41). Classical BD is in large part due to immunopathogenic damage to the nervous system by blood-borne inflammatory cells (49). However, responses to BDV infection vary according to differences in host-specific factors, e.g., species, animal strain, or age of the host at the time of infection (2, 24, 33, 48). For example, BDV-infected adult Lewis rats develop a highly immunopathogenic central nervous system disease characterized by acute, often fatal encephalitis with clinical signs of hyperactivity, aggression, and ataxia, followed by a chronic phase with resolving encephalitis and depressed behavior (19,41). In contrast, Lewis rats infected as neonates or as immunosuppressed adults do not develop significant inflammatory infiltrates in the brain and may develop behavioral signs of disease without becoming overtly ill (24,33,4...