Freetown: The infant had been treated at the Nixon hospital in Kailahun for diarrhoea and returned home, but he died after his health declined and he was readmitted for a blood transfusion, the officials said.
His parents and other family members in the Njaluahun tribal chiefdom have been placed in quarantine, the ministry said.
Health officials are monitoring an uncle who provided blood for the infant and investigating whether the sample he donated was the one used in the transfusion.
"The death has puzzled the chiefdom as the parents of the deceased have not been diagnosed as Ebola positive," Foday Sajuma, the manager of a local community radio station, told AFP.
Administrative areas such as counties and districts are declared "Ebola-free" by local authorities and the World Health Organization (WHO) once they have gone 42 days -- twice the maximum incubation period of the virus -- with no new cases.
"The area is in a sombre mood and a state of worry as residents are now resigned to begin a new Ebola countdown after recording a total of 111 days of zero Ebola," Sajuma told AFP.
The government's National Ebola Response Centre and the WHO have sent rapid response teams to Kailahun to trace anyone who may have had contact with the baby in a bid to contain the outbreak.
One of the deadliest viruses known to man, Ebola is spread through direct contact with the bodily fluids of an infected person showing symptoms such as fever or vomiting.
The epidemic has killed more than 10,000 people since it emerged in the forests of southern Guinea in December 2013 and spread to Liberia and then Sierra Leone.
Sierra Leone reported its first case in Kailahun, which borders Guinea, in May last year and the epidemic quickly spread throughout the country, with around 12,000 cases so far leading to more than 3,800 deaths.
The re-emergence of the virus at the epicentre of the outbreak comes with Sierra Leone seeing encouraging signs of a recovery, although the western area surrounding Freetown and parts of the north remain a worry.
Medical aid agency Doctors without Borders closed its Ebola clinic in Kailahun in February.
A baby has died of Ebola in a part of Sierra Leone where the outbreak began, dealing a blow to the recovery weeks after the district had eradicated the virus, officials said Monday.
The eastern district of Kailahun has been at the forefront of the country's recovery from the epidemic, having seen no new cases for more than three months and been declared "Ebola-free".
But health ministry officials confirmed a new case of the deadly tropical fever in a nine-month-old boy who tested positive after his death.
His parents and other family members in the Njaluahun tribal chiefdom have been placed in quarantine, the ministry said.
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"The death has puzzled the chiefdom as the parents of the deceased have not been diagnosed as Ebola positive," Foday Sajuma, the manager of a local community radio station, told AFP.
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"The area is in a sombre mood and a state of worry as residents are now resigned to begin a new Ebola countdown after recording a total of 111 days of zero Ebola," Sajuma told AFP.
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One of the deadliest viruses known to man, Ebola is spread through direct contact with the bodily fluids of an infected person showing symptoms such as fever or vomiting.
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Sierra Leone reported its first case in Kailahun, which borders Guinea, in May last year and the epidemic quickly spread throughout the country, with around 12,000 cases so far leading to more than 3,800 deaths.
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Medical aid agency Doctors without Borders closed its Ebola clinic in Kailahun in February.
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