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Did the physician who made the diagnosis visualize your throat?
Were there any associated problems with indigestion etc?
Those are important in determining the risk / benefit ratio of taking Omeperazole for long term.
Generally, the Proton pump inhibitors like Omeperazole have a good safety profile, and can be tolerated for a long time (as long as 3-6months).
However, it has to be medically justified by a diagnosis, requiring acid inhibition
So, if the diagnosis was acid reflux, and you cut down on the associated 6 S's called secretagogues.
Soda, Smoking, Spices, Spirits (alchohol), Spacing (your meal times), and Stress
The time it will take to heal depends on the status. Its variable
The least length of time for effective healing will be 6 weeks
The physician would has to re-evaluate you and compare how the throat looked prior to treatment
So do not be worried about the long term effects of the Omeperazole, if it is prescribed for GERD. The benefit far outweigh the risk of any adverse effect (unless you develop allergic reaction to it)
Please don't fail to let me know if you need any more clarifications
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