Hi,
Welcome to the ehealthforum and I am glad to help you out.
HPV and herpes are one of the most common sexually transmitted diseases. It can be due to having sex with multiple partners or with infected persons. Sometimes there are no symptoms at all of the infection and you cannot know until you do tests to diagnose it.
If your partner was not having any genital sores, it is not mandatory that she is free from STD's. You should get investigated for STD's like herpes, HPV and chlamydia. For these, you can opt for specific tests for Chlamydia which include Nucleic acid amplification tests (NAAT, to find the genetic material of Chlamydia), Nucleic acid hybridization tests (DNA probe test, Enzyme-linked immunosorbent assay (ELISA, EIA), Direct fluorescent antibody test (DFA) or chlamydia culture and herpes can be detected by culture of the virus, direct fluorescent antibody (DFA) studies to detect virus, skin biopsy, and polymerase chain reaction (PCR) to test for presence of viral DNA.
It is not mandatory to wait for 90 days and you can talk to your physician and get these tests done.
It is very difficult to precisely confirm a diagnosis without examination and investigations and the answer is based on the medical information provided. For exact diagnosis, you are requested to consult your doctor. I sincerely hope that helps. Take care.