Broad-Spectrum Detection of HPV in Male Genital Samples Using Target-Enriched Whole-Genome Sequencing

This pilot study applied a target-enriched whole-genome sequencing (eWGS) assay to characterize human papillomavirus (HPV) type diversity in 50 residual male genital swab samples. The assay generated high-quality sequencing data, with a mean of 10.5 million reads per sample. HPV was detected in 82% of samples, with a mean of 13.6 types per positive sample. A total of 237 unique HPV types were identified across four genera: 46 alpha, 55 beta, 135 gamma, and 1 mu. High-risk alpha types like HPV16, 18, and 31 were not common. A novel gamma type, now HPV229, was identified. The study suggests significantly higher HPV type diversity in males compared to females, warranting further investigation. Limitations include the use of residual samples without demographic data, potential storage effects, and the pilot nature of the study, which limits population representativeness. The findings demonstrate the utility of eWGS for broad-spectrum HPV surveillance.