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A spokesperson for the Northern Territory Department of Health confirmed that the deaths occurred in April and May but did not provide further details about the victims.
The alert follows the detection of the virus in mosquitoes in Darwin earlier this month, which led authorities to issue a public health advisory.
Murray Valley encephalitis is a rare but potentially severe mosquito-borne disease transmitted through the bite of infected mosquitoes.
Health officials say infections are most likely to occur between February and June, with cases typically peaking from March to May.
Symptoms can include severe headache, fever, nausea, vomiting, muscle aches, drowsiness, confusion, and seizures.
Authorities have urged residents and visitors across the Northern Territory to take preventive measures, including using insect repellents containing DEET or picaridin, wearing protective clothing, ensuring tents are mosquito-proof while camping, and avoiding mosquito-prone areas, especially after sunset.
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