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. 2023 Sep 21;15(9):1967.
doi: 10.3390/v15091967.

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

Tengguo Li  1 , Elizabeth R Unger  1 , Mangalathu S Rajeevan  1
Affiliations

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

Tengguo Li et al. Viruses. .

Abstract

Most human papillomavirus (HPV) surveillance studies target 30-50 of the more than 200 known types. We applied our recently described enriched whole-genome sequencing (eWGS) assay to demonstrate the impact of detecting all known and novel HPV types in male genital samples (n = 50). HPV was detected in nearly all (82%) samples, (mean number of types/samples 13.6; range 1-85), and nearly all HPV-positive samples included types in multiple genera (88%). A total of 560 HPV detections (237 unique HPV types: 46 alpha, 55 beta, 135 gamma, and 1 mu types) were made. The most frequently detected HPV types were alpha (HPV90, 43, and 74), beta (HPV115, 195, and 120), and gamma (HPV134, mSD2, and HPV50). High-risk alpha types (HPV16, 18, 31, 39, 52, and 58) were not common. A novel gamma type was identified (now officially HPV229) along with 90 unclassified types. This pilot study demonstrates the utility of the eWGS assay for broad-spectrum type detection and suggests a significantly higher type diversity in males compared to females that warrants further study.

Keywords: epithelial tropisms; male genital samples; universal HPV typing assay; vaccines.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Mapped Reads and Genome Coverage. Correlation shown for types by genus: (A) alpha, (B) beta, and (C) gamma. (D): Boxplot of depth of coverage by genus (log 2 scale; antilog of 10 to the base 2 = 210 = 1024).
Figure 2
Figure 2
Alpha HPV in Male Samples. Prevalence by type (A) and species (B). All alpha types detected were officially classified.
Figure 3
Figure 3
Beta HPV in Male Samples. Prevalence by type (A) and species (B). A total of 55 unique beta types were detected that included 11 unclassified types.
Figure 4
Figure 4
Gamma HPV in Male Samples. Prevalence by type ((A) 55 types classified, (B) 80 types unclassified) and species (C).
Figure 5
Figure 5
Overall HPV Prevalence in Male Samples. Alpha, beta, and gamma types are indicated by orange, blue, and purple bars, respectively.
Figure 6
Figure 6
Phylogenetic Tree of HPVs Detected in Male Samples. The tree is based on the L1 sequence of HPVs detected in this study, constructed using the tools at the PAVE EPSTEIME database. HPVs are grouped within alpha, beta, gamma, and mu (in green are gamma types with official classification). Tree branches in gray under gamma and beta indicate unclassified types. No unclassified types under alpha.
See this image and copyright information in PMC

References

    1. Williams J., Kostiuk M., Biron V.L. Molecular Detection Methods in HPV-Related Cancers. Front. Oncol. 2022;12:864820. doi: 10.3389/fonc.2022.864820. - DOI - PMC - PubMed
    1. Gheit T., Rollo F., Brancaccio R.N., Robitaille A., Galati L., Giuliani M., Latini A., Pichi B., Benevolo M., Cuenin C., et al. Oral Infection by Mucosal and Cutaneous Human Papillomaviruses in the Men Who Have Sex with Men from the OHMAR Study. Viruses. 2020;12:899. doi: 10.3390/v12080899. - DOI - PMC - PubMed
    1. Flores-Miramontes M.G., Olszewski D., Artaza-Irigaray C., Willemsen A., Bravo I.G., Vallejo-Ruiz V., Leal-Herrera Y.A., Pina-Sanchez P., Molina-Pineda A., Canton-Romero J.C., et al. Detection of Alpha, Beta, Gamma, and Unclassified Human Papillomaviruses in Cervical Cancer Samples from Mexican Women. Front. Cell Infect. Microbiol. 2020;10:234. doi: 10.3389/fcimb.2020.00234. - DOI - PMC - PubMed
    1. Agalliu I., Gapstur S., Chen Z., Wang T., Anderson R.L., Teras L., Kreimer A.R., Hayes R.B., Freedman N.D., Burk R.D. Associations of Oral alpha-, beta-, and gamma-Human Papillomavirus Types with Risk of Incident Head and Neck Cancer. JAMA Oncol. 2016;2:599–606. doi: 10.1001/jamaoncol.2015.5504. - DOI - PMC - PubMed
    1. Smelov V., Muwonge R., Sokolova O., McKay-Chopin S., Eklund C., Komyakov B., Gheit T. Beta and gamma human papillomaviruses in anal and genital sites among men: Prevalence and determinants. Sci. Rep. 2018;8:8241. doi: 10.1038/s41598-018-26589-w. - DOI - PMC - PubMed