I assuming you're a male but I guess I'm wrong? The swab could have caused some irritation of the vagina, but should not really give you pain on urination.
If you're having pain on urination it could be due to an different issue, but I couldn't say one way or the other.
Thanks. It wasn't a swab in the urethra however, which is why I'm worried about the pain. Especially on urination..
This is normal, and as far as I know there is no way to alleviate the pain. I'm unsure there is anything you can do to make inserting a large swab into your urethra less painful. The pain will fade in a day or so. Pain on urination is also normal due to the trauma. It too will fade with the pain.