Ok, I wanted to offer you some advice becuz my boyfriend and I went through the same thing, needless to say, we are still together and doing fine.
Now, I may bring up a few testy subjects with you but try not to close your mind to any of them... it is important to understand HPV and I must advise you to do as much research as you can on the virus and get ALL of the facts so that you can inform your girlfriend and help ease her fears.
Ok, so you are saying that you saw a wart before you were with your girlfriend? and you did not know it was a wart right? ( totally common, most people have no idea what they look like and assume that they are these big ugly warts, when in fact they look nothing like that) So is it safe to assume that there is no chance that your gf may have given it to you..right? I am not saying that she cheated but that may be what happened if you were just diagnosed... had to bring that up, sorry dude.
The odds are that you have already infected your gf, almost 100% if you have been with her for two years and have been having unprotected sex with her while you had visible warts.. but you may not want to throw that all in her direction at once.
Some facts are: 80% of the population carries this virus. If you have had three or more sexual partners you either carry the virus or have been exposed to it. Less that 30% of people that carry the virus EVER develop the warts. HPV is a transient virus and the body usually rids itself of the diease in 6months to two years after infection.
That last part was only recently discovered and many doctors do not even admit to it. The truth is that the medical community knows very little about HPV and that is why it is so prevelant.. like I said do your research! Read medical journals and studies on the internet.. it will really help you feel better about it all. Bottom line: it sucks have an STD, it sucks having to deal with warts, BUT, it is not the end of the world and honestly, it could have been a lot worse.
HPV is also weird becuz, there is no test for men that do not show visible warts so many men go around infecting people without even knowing that they carry it. Ok so, your girl goes in for paps every year? That is great and it is even more important that she continue to get those done. Having a negative pap does not mean that she does not have HPV. I had that similar idea and thought that I did not have HPV, I was misinformed...by my doctor, no less, so that just goes to show how little is known about this disease. I have normal paps but still have HPV. A abnormal pap means that she has tested positive for high risk HPV, the kind that CAN lead to cervical cancer but this is not as common as the low risk kind that causes the warts. She still has HPV but it is a great sign that her paps are normal...a really great sign.
Lastly, be honest with your girlfriend..please tell her and tell her that you did not know that you have the virus. My bf infected me and I was the one that developed the warts a short time after we started having unprotected sex... the truth is, you can never be sure who infected who becuz HPV can lay dormant in your body long after you have been infected so there is no use in pointing fingers... COme clean with your girl and be armed with facts to share with her to make her feel more at ease. There is nothing that you could have done to prevent this,, literally, nothing. That is why so much of the population has this virus. I hope this helps you and be sure to let us know how things are going.. don't be scared.... get the facts.