Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types

Abstract

Condylomas are caused by human papillomavirus (HPV), but may in rare cases be "negative for HPV" by PCR. Metagenomic sequencing can be used for an unbiased assessment of the presence of virus. Ten swab sample pools, each containing four cases of "HPV-negative" condylomas, were subjected to metagenomic sequencing. One pool contained Molluscum contagiosum. Five pools contained HPV, of which three pools contained novel putative HPV-types. The 12 samples in these three pools were sequenced individually. Six of these contained HPV and two contained Molluscum contagiosum. Altogether, 1337 HPV-related reads were detected, representing 23 novel putative Gammapapillomaviruses, 10 established HPV types (genital HPV types 6, 57, 58 and 66, Betapapillomavirus types 5, 105, 124, and Gammapapillomavirus types 50, 130, 150) and two described HPV sequences (KC7 and FA69). Complete genomes of Gammapillomavirus FA69 and SE87 were compiled. Metagenomic sequencing reveals that seemingly "HPV-negative" condylomas contain known and previously unknown HPV types.

Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets

“…We considered the approaches described in previous studies (19)(20)(21)(22)24) to identify HPV reads from the metagenomes, with modifications. We operated the analysis on the reads directly instead of using assembled contigs, because most reads in the HMP data sets could not be assembled into contigs.…”

“…In recent years, this method has been used for HPV detection in some human samples and has resulted in the identification of several novel HPV types (19)(20)(21)(22)(23)(24). Particularly, from condyloma samples negative for HPV using a traditional PCR method, abundant putative HPV sequences were found using metagenomics analysis (19).…”

Papillomavirus

“…This nested PCR system, validated on clinical samples, has proved to be a powerful tool for HPV detection even in environmental samples Iaconelli et al, 2015;La Rosa et al, 2015) . Recently, next generation sequencing has been shown to be effective in the detection of a wide range of HPVs, including novel types, in both clinical and environmental samples (Bibby & Peccia, 2013;Bzhalava et al, 2014;Cantalupo et al, 2011;Johansson et al, 2013;Kocjan et al, 2015). Since deep sequencing technologies are continuously evolving with increasing throughput and decreasing costs, it is likely that an expanding diversity of HPVs will continue to be revealed.…”

Prevalência e diversidade de beta-papilomavírus em amostras anogenitais e orais de homens do estudo HIM

“…Homens residentes no EUA (OR = 0,55, 95% intervalo de confiança [IC] de 0,38-0,80) e Brasil (OR = 0,49, 95% CI 0, 73) foram significativamente menos propensos a serem detectados com algum β-HPV no canal anal, comparado aos residentes no México. A idade foi marginalmente associada à maior prevalência de HPV na região do canal anal sendo que de homens mais velhos (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)OR = 1,30,95% CI 0,82;OR = 1,59,95% CI 0,58) foram mais propensos a serem positivos para DNA de β-HPV, comparado a homens mais jovens (18-30 anos). A prevalência de algum β-HPV na cavidade oral também foi significativamente associada ao país de residência e idade.…”

“…Samples were tested for PCR amplification with PGMY09/11 primers, and HPV genotyping was conducted with the Roche Linear Array (Roche Molecular Diagnostics, Alameda, CA, USA), which is able to discriminate 37 α-HPV types (oncogenic types 16,18,31,33,35,39,45,51,52,56,58,59, and 66; non-oncogenic types 6,11,26,40,42,53,54,55,61,62,64,[67][68][69][70][71][72][73][81][82][83][84]IS39,and CP6108) [14]. Samples that tested PCR-positive and Linear Array-negative with all specific HPV probes were considered to be unclassified and included in the present study.…”