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Although HAART can suppress genital shedding and sexual transmission of HIV, men who have sex with men (MSM) have experienced a resurgent HIV epidemic in the HAART era. Many HIV-infected MSM continue to engage in unsafe sex, and sexually transmitted infections (STIs) or other factors may promote genital HIV shedding and transmission in this population despite HAART. In this study, we determined the prevalence of seminal HIV shedding in HIV-infected MSM on stable HAART, and its relationship with a number of clinical, behavioral and biological variables.Sexually active HIV-infected men using HAART were recruited from an MSM health clinic to provide semen and blood samples.HIV levels were assessed in paired semen and blood samples by PCR. Clinical and behavioral data were obtained from medical records and questionnaires. Herpes simplex virus 2 (HSV-2) serostatus, seminal HSV-2 DNA, and markers of genital inflammation were measured using standard laboratory methods.Overall, HIV-1 was detected in 18 of 101 (18%) blood and 30 of 101 (30%) semen samples. Of 83 men with undetectable HIV in blood plasma, 25% had HIV in semen with copy numbers ranging from 80 to 2560. Multivariate analysis identified STI/urethritis (P = 0.003), tumor necrosis factor α (P = 0.0003), and unprotected insertive anal sex with an HIV-infected partner (P = 0.007) as independent predictors of seminal HIV detection.STIs and genital inflammation can partially override the suppressive effect of HAART on seminal HIV shedding in sexually active HIV-infected MSM. Low seminal HIV titers could potentially pose a transmission risk in MSM, who are highly susceptible to HIV infection.