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Akhil, a native of Karassery, who was undergoing treatment at the Kozhikode Medical college hospital (KMCH) since May 29, died last night, the official said.
Two more persons, confirmed of having contracted the virus are being treated at KMCH, he said.
Besides, 1,353 people who had been in contact with the affected persons before the confirmation of the disease, are under observation, the official said.
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The outbreak of the Nipah virus infection, a newly emerging zoonosis that causes severe disease in both animals and humans, is suspected to be from an unused well in Perambra which was infested with bats.
The natural host of the virus is believed to be fruit bats of the Pteropodidae family, Pteropus genus.