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If anything you can make a better case about why you want to pursue a research career as you have been exposed to more medical background / how research has shaped current medical care / now you are more interested in being a physician scientist (maybe you never met them before/didnt consider being one yourself until now). You still need legitimate reasons as to why you want to pursue the PhD. So think about that in a lot of detail (and specifically why you would be successful during the PhD). Have some potential research mentors in mind.
 
At my school, the general rule for internal applicants is that they are judged by the same standards as those who are applying MD/PhD from the beginning. If someone wouldn't have been accepted as an external applicant, they won't be accepted as an internal one.

Make sure that you can talk about your past research experiences intelligently and passionately. Make sure you have a good answer for the classic "why MD/PhD question". As for explaining why you didn't apply MD/PhD from the beginning, just be honest. If you liked your school so much that you wanted to maximize your chances of acceptance by applying MD-only, but were always hoping to apply internally, that sounds perfectly reasonable to me.
 
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