Semliki Forest virus (SFV) is a mosquito-transmitted pathogen of small rodents, and infection of adult mice with SFV4, a neurovirulent strain of SFV, leads to lethal encephalitis in a few days, whereas mice infected with the avirulent A7(74) strain remain asymptomatic. In adult neurons, A7(74) is unable to form virions and hence does not reach a critical threshold of neuronal damage. To elucidate the molecular mechanisms of neurovirulence, we have cloned and sequenced the entire 11,758-nucleotide genome of A7(74) and compared it to the highly neurovirulent SFV4 virus. We found several sequence differences and sought to localize determinants conferring the neuropathogenicity by using a panel of chimeras between SFV4 and a cloned recombinant, rA774. We first localized virulence determinants in the nonstructural region by showing that rA774 structural genes combined with the SFV4 nonstructural genome produced a highly virulent virus, while a reciprocal recombinant was asymptomatic. In addition to several amino acid mutations in the nonstructural region, the nsp3 gene of rA774 displayed an opal termination codon and an in-frame 21-nucleotide deletion close to the nsp4 junction. Replacement in rA774 of the entire nsp3 gene with that of SFV4 reconstituted the virulent phenotype, whereas an arginine at the opal position significantly increased virulence, leading to clinical symptoms in mice. Completion of the nsp3 deletion in rA774 did not increase virulence. We conclude that the opal codon and amino acid mutations other than the deleted residues are mainly responsible for the attenuation of A7(74) and that the attenuating determinants reside entirely in the nonstructural region.Semliki Forest virus (SFV) is an enveloped positive-stranded RNA virus of the family Togaviridae. The SFV prototype was isolated in 1942 from a pool of mosquitoes in Uganda (40). The A7(74) strain (4) is a derivative of an SFV strain isolated from mosquitoes in Mozambique in 1959 (26). Several strains of SFV, such as L10 (4) and SFV4 (24), cause lethal encephalitis in mice of all ages, leading to death of the animals in a few days (3, 11), whereas A7(74) infection of adult mice is asymptomatic per se but leads to axonal demyelination mediated by CD8 ϩ T cells (2). However, the severity of A7(74) infection is strictly age dependent, being lethal for neonatal mice less than 2 weeks old (8, 27), probably because the strain is capable of virion formation in propagating neurons, unlike in mature neurons (27).SFV nonstructural proteins (nsP) are translated as a polyprotein (nsP1234) from the genomic 42S RNA, and they form essential components of viral RNA replication and transcription complexes (14). The nsP1 protein is a methyl-and guanylyltransferase (1, 18), whereas the nsP2 is a proteinase (45) and nucleoside triphosphatase (33). The nsp3 gene product is a phosphoprotein, and it has been proposed to function together with nsP1 in anchoring the replication complex proteins to cytoplasmic membrane structures (30, 31). In Sindbis virus (SIN), p123 a...