What happens to a Teenage girl who has broken her virginity

Im a 19 year old male who has taken my 17 year old girlfriend virginity on december 14,2012. We used protection which we know would prevent us from disease & prevent her from not getting prenant. I did now c-um & the condom did not break so later in the month she has seen her period Decmber 27,2012, she had a change in cycle which made us a bit worried.

Two(2) months after the  sex she has text me telling me that she has missed hher period twice & i dont know what is the cause of it because i didnt c-um & the condom didnt break & she's telling me I'm the only one she has had sex with. Im now worried because she is now telling me she's pregnant & i dont understand how because she has seen her period december 27,2012, and she says she has only had sex once (1). She has done a home pregnancy test which says she is pregnant.

Is this a change in her cycle or a change in her body structure i urgently need a reply from you please thanks for your help.