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Prolonged cough can cause straining in the stomach muscles and lead to abdominal pain at times.Some suggestions for you:
Take a glass of water and mix 1 tbsp honey and half lemon juice in it.It will help in throat infection.
Drink lots of water.
Massage the abdominal area your self so that the starined muscles are relaxed.
If the pain persists or increases in intensity consider visiting a Physician for clinical examination.
Take Care!