How Do I Deal With This Dilemma

Long story short.... Left my girlfriend 8 1/2 months ago for a work assignment. I came back just in time to see my son born. We haven't had sex as she needed time to heal. Just last week I had an outbreak of warts in my genital area. I was told that I have genital warts and understand that I could have had it for years without knowing it. But as her healing time is coming to a close she is mentioning sex and counting down to the exact day and hour that we have the green light. The only thing that concerns me is that when I tell her I have this is that she will think I was cheating while I was away no matter how much I explain that I could have been carrying this virus for years. I care about her a lot and I also don't want her to get vindictive and use my newborn son as a weapon. How do I handle this?