About a quarter of students attended the school on Wednesday
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About 900 pupils were given the day off school on Wednesday following the death of a 10-year-old girl from meningitis.
Roger Kaye, head teacher of Tiverton High School, made the offer to pupils to give them the opportunity for "calm reflection".
The girl, who has not been named yet, died from the illness early on Monday morning.
About 300 pupils decided to attend lessons, and teachers say the other students are expected to be back in school as normal on Thursday.
All pupils in the girl's class at the school have been offered antibiotics and on Tuesday all 1,200 pupils and 100 staff at the school were offered the same treatment.
All pupils at the school have been offered antibiotics
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It is the third case of meningitis in the Tiverton area within the last two weeks.
Two boys, one from Tiverton High School, were admitted to hospital with the disease. Both have since been discharged.
Health officials are also tracing those who were at a birthday party with the girl last week and a disco in Tiverton on 30 January.
Dr Mark Kealy, a consultant in communicable disease control at the South West Peninsula Health Authority, said: "We would hope that the risk would be very small.
Laboratory tests
"If there are carriers in the school, and presumably there are, we will eradicate any bacteria from their nose and throat and prevent any further cases.
"Nevertheless we should emphasise that people should be on the lookout for symptoms.
"This isn't a cure, it's trying to wipe the slate clean and stop it from being spread."
Laboratory tests showed the cause of the girl's death was meningococcal meningitis.