PEP is a relatively new protocol that attempts to prevent a person from becoming HIV infected by administering anitviral medications after a significant exposure to the virus.
PEP is complicated.
It is still not clear if PEP actually works, the medications' side-effects are very difficult for many people to tolerate, and insurance companies don't generally cover the cost of medication. It's also hard to find professionals who actually use PEP protocols. If you feel that your partner meets the PEP criteria and would like to take medication, you should talk with your doctor. You also need to take care of each other emotionally during this difficult period. If praying works for you, then seek out spiritual counseling and guidance.