I also had chlamydia and I now still have a reddish fungal infection on the shaft of my penis and scrotum. I have used Lotrimin for a week and it has not improved much at all. Both of those were negative. I was told that if I had been going through ARS then the PCR test would have shown a large amount of the virus.
Symptoms usually occur two-four weeks after infection.
One study found that average length of symptoms to be 22 days. The literature does not indicate a fungal infection on the penis as the more common symptom of primary infection, but it is not ruled out. A negative result on both your PCR and antibody tests is a good sign, although PCR tests as diagnostic tools are not as reliable as an antibody test at three months. A PCR test is highly sensitive and would be likely to detect high levels of virus associated with primary infection. However, PCR tests should be used wisely and in conjunction with other tests when diagnosing HIV infection.