A rigorous exploration of anal HPV genotypes using a next‐generation sequencing (NGS) approach in HIV‐infected men who have sex with men at risk for developing anal cancer

Abstract

Background: There are no HPV-based measures for managing anal cancer (AC) in HIV-infected (HIV+) men who have sex with men (MSM) because of the high positivity of high-risk (HR)-HPVs. As next-generation sequencing (NGS) is able to describe the composition of HPVs as percent (%) reads rather than positive vs negative results, we used NGS approach to detect HPVs in anal samples of HIV+ MSM to test its ability to differentiate those who are diagnosed with atypical squamous cells of unknown significance or greater (ASCUS+) from those who are free of such lesions and to understand the burden of HPV infections in relation to HPV vaccines. Methods: Study included 81 HIV+ MSM characterized for demographics, patientreported outcome measures, HIV related laboratory measures and anal cytology.We summarized NGS HPV data using % read cut points (>0%->30%) and tested the relationship between % reads of HR-HPVs and risk of ASCUS+ using logistic regression. Results: Forty-six HPVs were detected at the >0% read cut point. The prevalence of any HR-HPVs varied from 100% to 40% with >0% to >30% reads while ≥99% were infected with HR-HPVs included or not included in the 9 valent HPV vaccine at the >0% read cut point. MSM with >30% HR-HPV reads were 4.5 times more likely to be diagnosed with ASCUS+ compared to ≤30% reads (P = .033). Conclusion: NGS-based approach is more accurate than PCR-based HPV testing for identifying HIV+ MSM at risk for developing AC. We raise the concern regarding the efficacy of current HPV vaccines for preventing AC in this high-risk population. K E Y W O R D Sanal cytology, HIV, HPV, MSM, next-generation sequencing 808 | PIYATHILAKE ET AL.

Role of Low-Risk HPV PCR Monoinfection in Screening for HSIL and Anal Cancer in Men Who Have Sex with Men Living with HIV

“…In regard to HIV infection, their viroimmunological status was excellent, with only 4.1% in virologic failure and a median CD4 count of 698.9 cells; 71.2% were infected with LR genotypes, 74% with HR genotypes, and 56% were coinfected with LR and HR genotypes. Less than half of the participants had normal anal mucosa, around one-tenth had HSIL at enrolment, and three (0.6%) had anal cancer, a similar profile to that of other European cohorts [ 10 ], and even of a North American study population that mainly differed in ethnic make-up, with a predominance of Afro-Americans [ 11 ]…”

Human papillomavirus sequencing reveals its usefulness for the management of HIV‐infected women at risk for developing cervical cancer

“…Analysis of various HPV sequences was accomplished with deep sequencing using 20 ng of DNA from each sample as previously described 18 . Briefly, the first round of polymerase chain reaction (PCR) was performed with PGMY11/09 primers and the second round with nested GP5+/GP6+ primers that also contained sequences at their 5′ termini to incorporate sequences necessary for cluster formation on the MiSeq flowcells and to include sequences for a dual indexing scheme.…”

HPV genotyping in clinical samples using long‐read single‐molecule real‐time sequencing

“…Several teams have developed and evaluated PCR-nextgeneration sequencing techniques for HPV typing using second-generation techniques for identifying short sequences mainly in the L1 region. [14][15][16][17][18][19][20][21] and in the E6/E7 region. 22 The advent of third-generation sequencing technology, Pacific Bioscience (PacBio) single-molecule realtime (SMRT) or Oxford Nanopore Technology, has led to the possibility of sequencing long fragments and studying haplotypes.…”

“…In recent years, the development of high‐throughput sequencing techniques has made it easier to obtain multiple sequences from a single sample. Several teams have developed and evaluated PCR‐next‐generation sequencing techniques for HPV typing using second‐generation techniques for identifying short sequences mainly in the L1 region 14–21 . and in the E6/E7 region 22 .…”