Forty school children were killed when a train crashed with a bus south of Egypt's capital on Saturday, according to the official state news agency.
The train reportedly hit the school bus from the city of Manfalut, near Assiut.
The city's governor has ordered an enquiry into the incident.
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The pair, believed to be the boy's mother and stepfather, were held after the five-year-old's lifeless body was discovered in a lagoon.