Hi, and thanks for your medical question on eHealth forum!
Take a pregnancy test first as you missed periods. The discharge can be due to pregnancy. HPV can cause just cervical inflammation and infection and this can cause brown discharge. If there is change is cells of cervix, then low grade squamous intraepithelial lesion, or LGSIL are most common and easily treatable by cauterization. Most are treated through a waitt and watch policy. So if you do not have warts, then probably you had LGSIL in PAP which is linked to HPV.
There are no actual tests for HPV except for showing presence of virus DNA in lesions. Please discuss in detail with your gynecologist. Hope this helps. Take care!