Animals with encephalitis had higher levels of viral DNA in both the brainstem (A, neonates n=13, juveniles n=5, SIVnoE adults n=19, SIVE adults n=9; p<0.0001) and frontal lobe (B, neonates n=12, juveniles n=5, SIVnoE adults n=20, SIVE adults n=9; p<0.0013) than any of the other groups of animals. There was no significant difference between the non-encephalitic groups. To determine if there was ongoing viral replication, viral RNA was determined. Encephalitic animals had higher RNA levels than the other groups in both brainstem (C, neonates n=12, juveniles n=5, SIVnoE adults n=13, SIVE adults n=6; p<0,0001) and frontal lobe (D, neonates n=13, juveniles n=5, SIVnoE n=14, SIVE adults n=6; p<0.0004). There was also higher viral RNA in adults, even without encephalitis, than juvenile animals (C).