Comparison of urine and semen samples for HPV detection: a cross-sectional study in fertility clinic patients

Human papillomavirus (HPV) is a prevalent sexually transmitted infection linked to genital warts and various cancers. While effective screening methods exist for women, detecting HPV in men remains challenging due to asymptomatic infections and the lack of standardized, non-invasive diagnostic tools. This study aimed to assess the correlation between HPV DNA detection in urine and semen samples from men attending a fertility clinic in Ecuador. This cross-sectional study included 106 sexually active male patients referred for semen analysis at the Fertility Unit of Hospital del Río, Cuenca, Ecuador, between June 2024 and March 2025. Each participant provided paired semen and urine samples, which were analyzed for HPV genotyping. Sociodemographic and behavioral data were also collected. HPV DNA was detected in 15% of semen samples and 9.4% of urine samples. Both low- and high-risk genotypes were identified in semen and urine. In semen samples, high-risk HPV was detected in 9.4% and low-risk HPV in 5.7%. In urine, high-risk HPV was detected in 8.5% and low-risk HPV in 0.9% of samples. Among high-risk genotypes, HPV 58 was the most frequent in urine (20%), while HPV 81 was the most frequent in semen (19%). Genotypes such as HPV 16, 18, 39, 52, and 66 were detected exclusively in semen. Compared with semen sampling, urine sampling showed a sensitivity of 37.5% and a specificity of 95%. Agreement between the two sample types was fair (kappa = 0.39). Although urine sampling offers a non-invasive option, its limited sensitivity restricts its utility as an HPV detection method in asymptomatic men. Semen analysis provides higher detection rates and may be more reliable for HPV screening in male fertility populations.