Welcome to the Forum. As I suspect you know, Bowenoid papulosis is an HPV 16-associated problem involving the skin of the penis. While most of the time it is a benign process, on rare occasions it can gradually progress to cancer of the penile skin. To my knowledge, there are no data on the prevalence of HPV in the urine because testing is not routine. Presumably your positive urine test is a reflection of infection of the urethral lining. In women who are the group best studied, HPV infections tend to resolve over time, sometimes taking several years to do so. I have not personally managed urethral HPV infections and given your past diagnosis of Bowenoid papulosis, I would be inclined to follow this over time. If the positive urine test persists, further evaluation, primarily to rule out cancer or pre-cancerous lesions. I would suggest that your urologist and/or dermatologist may have colleagues within their professional networks who might be best prepared to recommend the way forward for you. In answer to your specific questions:
1. Does this positive test mean there may be actual lesions inside my urethra?
No. the presence of HPV in your urethra may not be associated with visible lesions.
2. Can this lead to cancer? HPV 16 is a high risk for cancer
For HPV most of the data are from women in whom 'high" risk means that a small proportion (less than 3%) of untreated infections may progress to cancer over time. I have no doubt that urethral infections occur and urethral carcinoma can follow but would guess that this too is rare, particularly given the high frequency of HPV 16 infections and the rarity of urethral carcinoma. Urethral cancer is best diagnoses by biopsy performed using urethroscopy.
3. I assume that since I have a positive result 5 years after the spots on the penile shaft that this means the virus is persistent and that my body will not clear it?
Perhaps. We can't be sure.
4. Is a urethroscopy the only way to identify lesions if there are any?
Urethroscopy looking for lesions and a biopsy would seem to be reasonable although your urologist is the best source of information on this.
5. What would you recommend as a course of action or treatment?
If lesions are present and if they show precancerous lesions there are a variety of treatment approaches which again, I would look to your urologist for advice on. If the are no lesions or if lesions are present and no precancerous changes are present, it may be reasonable to follow the lesions with periodic repeat testing to see if it clears without therapy.
sorry I don't have more information on this topic. Hope my comments are helpful. EWH