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The virus has infected more than 150,000 people worldwide and killed over 5,600.
The chartered flight was carrying four government workers and the pilot.
In a video, the man repeatedly jabs at the back of the seat. On Twitter, a debate ensued about airplane etiquette.
The airline has pulled three 737 NG jets from service but says it will minimise customer impact.
William joked that he was flying the aircraft.
Flight JT610 took off around 6.20 a.m. and was due to have landed in the capital of the Bangka-Belitung tin mining hub at 7.20 a.m.