So your sample has a prevalence higher than most samples and you think your PPV estimates may be mis-leading?

If so, you have selection bias in your sampling, since it does not appear to be random from the population at large. Yes, prevalence can mess up the horizontal calculations. Can you just report this, or are you using this results yourself. Depending on things or reporting, I wonder if you can mess around with the constant term in a logistic regression model to account for this, though I am not sure you can easily get PPV out of your logistic model.