A 4-year-old aboriginal boy developed encephalitis due to Murray Valley enc
ephalitis virus (MVE) following an earlier infection with Kunjin virus (KUN
). The illness was severe, resulting in cerebral atrophy and profound physi
cal and intellectual disability. The earlier KUN infection complicated his
serological profile and delayed antibody responses to MVE. By contrast, the
reverse transcriptase-polymerase chain reaction (RT-PCR) assay detected MV
E in serum 3 days after the onset of illness and 4 days before the appearan
ce of MVE-specific IgM. We suggest that MVE-specific RT-PCR provides rapid
and specific diagnosis of MVE and should be used more widely for the diagno
sis of acute viral encephalitis in cases originating from flavivirus endemi
c areas.