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The samples of the boy, which were sent to the Pune National Institute of Virology, confirmed the presence of Nipah virus.
The Central Government has rushed a team of National Centre for Disease Control to the state, which will be reaching on Sunday.
The team will provide technical support to the state, the ministry said.
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The measures also include active contact tracing for any contacts in the past 12 days, strict quarantine of the contacts and isolation of any suspects and collection and transportation of samples for lab testing, the ministry said.
Nipah virus is spread by saliva of the fruit bats.
In 2018 also, there was a Nipah outbreak in Kozhikode and Malappuram districts of Kerala.