HPV is an unlikely cause for pain with or after intercourse. It's associated with abnormal pap tests, which may require further investigation—like the biopsy you say you had. Much less commonly, it can cause genital warts. If the warts happen to be at the opening of the vagina, they can become irritated and cause discomfort, but that's really very rare.
It's more likely the discomfort is related to the atrophic changes of menopause, which you may not have been aware of between relationships. In the absence of estrogen, the tissues become thin and less distensible—meaning less stretchy and able to expand—and also more fragile and easily injured. This can happen even if you don't perceive dryness.
You didn't say how long you've been sexually active; this problem may resolve itself: It's the opposite of "use it or lose it"! But because menopausal tissues don't rejuvenate quite as well as younger, fully estrogenized tissues do, you might consider using a moisturizer or localized estrogen. But I wouldn't worry about HPV being a cause.