Putative Human Papillomavirus Research Articles

HPV-YAP1 oncogenic alliance drives malignant transformation of fallopian tube epithelial cells

High grade serous ovarian carcinoma (HGSOC) is the most common and aggressive ovarian malignancy. Accumulating evidence indicates that HGSOC may originate from human fallopian tube epithelial cells (FTECs), although the exact pathogen(s) and/or molecular mechanism underlying the malignant transformation of FTECs is unclear. Here we show that human papillomavirus (HPV), which could reach FTECs via retrograde menstruation or sperm-carrying, interacts with the yes-associated protein 1 (YAP1) to drive the malignant transformation of FTECs. HPV prevents FTECs from natural replicative and YAP1-induced senescence, thereby promoting YAP1-induced malignant transformation of FTECs. HPV also stimulates proliferation and drives metastasis of YAP1-transformed FTECs. YAP1, in turn, stimulates the expression of the putative HPV receptors and suppresses the innate immune system to facilitate HPV acquisition. These findings provide critical clues for developing new strategies to prevent and treat HGSOC.

Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis.

Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.

Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues.

Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01.

Determination of human papillomavirus type in archival tissue specimens of invasive cervical cancer using molecular mapping and E6/E7-based polymerase chain reaction.

In our previous study, an L1-based human papillomavirus (HPV) test using liquid-based cytology revealed that some invasive cervical cancers (ICC) exhibited multiple HPV types or harbored no HPV DNA. Here, molecular mapping of formalin-fixed paraffin-embedded cancer tissue specimens from the same patients were conducted to confirm these observations. Among 377 ICC cases, 73 eligible specimens (9 positive for multiple HPV types, 16 negative for HPV, and 48 positive for a single HPV type from the previous study) were reexamined by manual microdissection of cancer lesions, then subjected to HPV genotyping using the uniplex E6/E7 polymerase-chain-reaction method to detect all high-risk and potentially high-risk HPV types. The HPV typing results were confirmed in 52 of 73 cancer cases; among the 21 remaining cases, 15 were discordant and 6 were partially concordant. In total, 8 of 16 (50%) HPV-negative samples became positive; 6 were positive for HPV16 and 2 were positive for HPV67. Moreover, two samples previously positive for HPV6 and HPV53 were negative for HPV. All nine cancers with multiple HPV types were found to harbor only a single HPV type. In total, 63 cancer tissues exhibited a single HPV type. HPV16 and HPV18 were detected in squamous cell carcinoma (SCC) and adenocarcinoma (ADC). Alpha-5 (HPV82), -6 (HPV56), and -9 (HPV31/52/67) HPV types were detected in SCC, whereas Alpha-7 (HPV59/68) types were detected in ADC and adenosquamous carcinoma (ADSCC). These findings suggested that the different HPV types induced different histological cancers. Furthermore, all SCCs and 10 of 11 usual-type ADCs were positive for high-risk HPV types, supporting the use of HPV screening for the detection of these cancers and associated premalignant lesions. HPV16 is likely to remain undetected in some cervical cancer tissues because of low viral-copy-numbers. Putative high-risk HPV types (e.g., HPV67 and HPV82) might be high risk in Japan.

Misclassifications in human papillomavirus databases

We assessed the quality of human papillomavirus (HPV) sequences in GenBank by analyzing the possible presence of chimeras, “wrong-assembled” contigs and errors in taxonomy using an open-source script (HPVChimera_Gb) that compared 25 638 HPV-related nucleotide sequences in GenBank with the 221 numbered HPV types and another 220 complete HPV sequences. There were 110 sequences with taxonomy/naming errors (sequences reported as another HPV type than the one they corresponded to) and 1318 possibly chimeric sequences. Manual analysis found plausible explanations for most of them (e.g. sequence covering an integration site) but 114 sequences appeared to be chimeras (96/114 were already flagged as “unverified” by GenBank) and 13 had taxonomy/naming errors. When comparing all correct HPV sequences in GenBank, there appeared to exist about 800 unique putative HPV types. Systematic and regular work towards eliminating chimeric sequences and taxonomy/naming errors could increase the quality and order in HPV research.

Kissing, Saliva and Human Papilloma Virus: Principles, Practices, and Prophylaxis

Introduction: Kissing is a globally practiced form of communication, yet saliva is often deemed a harmless bodily fluid. Many viruses thrive in salivary and oro-pharyngeal lymphoid cells. These viruses include Human Papilloma Virus (HPV), Human Herpes Viruses, Epstein –Barr, HIV, Polio and others, and are transmitted between people when kissing. Aim: This appraisal (1)assesses socially sanctioned kissing habits, (2) examines the presence of Human Papilloma Virus [HPV] in saliva and salivary tests for HPV, (3) reviews protection from HPV vaccines, (4)deconstructs attitudes and behavior, and critiques the oncogenic potential of HPV morbidity from peri-osculation practices. Materials and Methods: Clinical- tests for putative HPV viruses in oro-pharyngeal cancers use saliva to detect HPV oncogenic types; these re-affirm presence of HPV’s in saliva, and their causal relationship to the majority of head and neck cancers. Conclusion: Although frequency of new infections from kissing is unknown, this critique suggests caution against random kissing, encourages use of HPV vaccination for prophylaxis, and indicates that this may moderate HPV and viral transmission, with consequent reduction of HPV morbidity and mortality.

Oral Infection by Mucosal and Cutaneous Human Papillomaviruses in the Men Who Have Sex with Men from the OHMAR Study.

Both mucosal and cutaneous Human Papillomaviruses (HPVs) can be detected in the oral cavity, but investigations regarding the epidemiology of cutaneous HPVs at this site are scarce. We assessed mucosal (alpha) and cutaneous (beta and gamma) HPV infection in oral samples of HIV-infected and uninfected men who have sex with men (MSM). Oral rinse-and-gargles were collected from 310 MSM. Alpha HPVs were detected using the Linear Array, whereas beta and gamma HPVs were detected using multiplex PCR and Luminex technology. An amplicon-based next-generation sequencing (NGS) protocol was applied to a subset of samples collected from 30 HIV-uninfected and 30 HIV-infected MSM. Beta HPVs were significantly more common than alpha types (53.8% vs. 23.9% for HIV-infected subjects, p < 0.0001; 50.3% vs. 17.1% for HIV-uninfected subjects, p < 0.0001). Gamma HPVs were also frequently detected (30.8% and 25.9% in HIV-infected and uninfected MSM, respectively). NGS produced 2,620,725 reads representative of 146 known HPVs (16 alpha-PVs, 53 beta-PVs, 76 gamma-PVs, one unclassified) and eight putative new HPVs, taxonomically assigned to the beta genus. The oral cavity contains a wide spectrum of HPVs, with beta types representing the predominant genus. The prevalence of beta and gamma HPVs is high even in immunorestored HIV-infected individuals. NGS confirmed the abundance of cutaneous HPVs and identified some putative novel beta HPVs. This study confirms that cutaneous HPVs are frequently present at mucosal sites and highlights that their pathological role deserves further investigation since it may not be limited to skin lesions.

Abstract B56: YAP1 inhibits host cell immunity and increases human papillomavirus (HPV) infection to drive cervical tumorigenesis

Abstract Although human papillomavirus (HPV) is believed to be the major causative agent for cervical cancer, accumulating evidence indicates that HPV alone is insufficient to induce cervical cancer. The molecular mechanisms underlying cervical cancer development remain unclear. In the present study, we provide evidence showing that the Hippo/YAP pathway plays a critical role in cervical carcinogenesis. We found that genetic alteration of the Hippo/YAP pathway frequently occurred in human cervical cancer patients and was associated with poor prognosis of these patients. Keratin 14 promoter-driven expression of constitutively active YAP1 (YAP S127A) in mouse cervical epithelial cells induced invasive cervical squamous cell carcinoma (CVSCC), suggesting that hyperactivation of YAP1 is sufficient to induce cervical cancer. Importantly, hyperactivation of YAP1 in cervical epithelial cells not only increased the putative HPV receptor molecules and cellular susceptibility to HPV infection, but also disrupted the host cell innate immune system, resulting in failure of HPV viral recognition, suppression of type I IFN production, inhibition of the IFNRs/JAKs/STATs pathway, and blockage of production of antiviral interferon-stimulated genes. Cervical epithelial-specific YAP1 and HPV double knockin mouse models showed that YAP1 synergizes with HPV to promote the initiation and progression of CVSCC. The present study demonstrates that the Hippo/YAP pathway plays a central role in the development of CVSCC and the synergism between hyperactivated YAP1 and high-risk HPV may be the key driver of cervical cancer development. The Hippo/YAP signaling pathway may represent a promising target for developing novel strategies to prevent and treat cervical cancer. Citation Format: Xiangmin Lv, Chunbo He, Cong Huang, Hongbo Wang, Li Chen, Peichao Chen, John S. DavisS, Bo R. Rueda, Cheng Wang. YAP1 inhibits host cell immunity and increases human papillomavirus (HPV) infection to drive cervical tumorigenesis [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B56.

Broad-Range Papillomavirus Transcriptome as a Biomarker of Papillomavirus-Associated Cervical High-Grade Cytology

Human papillomaviruses (HPVs) are responsible for >99% of cervical cancers. Molecular diagnostic tests based on the detection of viral DNA or RNA have low positive predictive values for the identification of cancer or precancerous lesions. Triage with the Papanicolaou test lacks sensitivity; and even when combined with molecular detection of high-risk HPV, this results in a significant number of unnecessary colposcopies. We have developed a broad-range detection test of HPV transcripts to take a snapshot of the transcriptome of 16 high-risk or putative high-risk HPVs in cervical lesions (HPVs 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68, 73, and 82). The purpose of this novel molecular assay, named HPV RNA-Seq, is to detect and type HPV-positive samples and to determine a combination of HPV reads at certain specific viral spliced junctions that can better correlate with high-grade cytology, reflecting the presence of precancerous cells. In a proof-of-concept study conducted on 55 patients, starting from cervical smears, we have shown that HPV RNA-Seq can detect papillomaviruses with performances comparable to a widely used HPV reference molecular diagnostic kit; and a combination of the number of sequencing reads at specific early versus late HPV transcripts can be used as a marker of high-grade cytology, with encouraging diagnostic performances as a triage test.

Abstract LB-A01: Yes-associated protein 1 regulates cervical cancer initiation and progression via suppressing innate immunity and increasing cell susceptibility to human papillomavirus infection

Abstract Introduction: Although human Papillomavirus (HPV) has been identified as a causative reagent for cervical cancer (CVC), accumulating evidence indicates that HPV alone is insufficient to induce CVC. The molecular mechanisms underlying CVC development are largely unknown. Our previous in vitro studies indicated that YAP1, the major effector of the Hippo pathway, interacts with HPV to drive the progression of CVC. However, whether the Hippo/YAP1 pathway also regulates cervical carcinogenesis in vivo is unknown. Aims: To examine the molecular mechanism(s) by which the Hippo/YAP pathway interacts with HPV to regulate the cervical carcinogenesis. Methods: The cBioportal for Cancer Genomics, an online tool developed to visualize The Cancer Genomic Atlas (TCGA) studies, was used to analyze alterations of the Hippo pathway in human CVC. Primary cervical epithelial cells and cervical cancer cell lines were used to determine effects of YAP1 on cell susceptibility to HPV infection. KRT14-YAPS127A mice, which express constitutively active YAP1 (YAPS127A) in cervical epithelial cells under doxycycline (Dox) induction, and KRT14-E6/E7-YAPS127A mice, which express both HPV E6/E7 and YAPS127A in cervical epithelial cells under Dox induction, were used to examine the role of YAP1 gene in cervical carcinogenesis. Results: Multidimensional cancer genomic data showed that disruption of the Hippo signaling pathway is a common event in human CVC, which is featured by frequent amplification and up-regulation of oncogenes and deletion/mutation of tumor suppressors. Moreover, the disrupted Hippo pathway is associated with poor prognosis of CVC patients. Dox-induced expression of YAPS127A in KRT14-YAPS127A mouse cervical epithelial cells resulted in neoplasia of cervical epithelium within 2 months. Most KRT14-YAPS127A mice developed invasive CVC after induction with dox for 6 months. Metastatic spread of CVC induced urethral and outlet obstruction in some KRT14-YAPS127A mice. Around 50% of KRT14-YAPS127A mice died of CVC within 16 months of Dox induction. Histological analysis revealed that KRT14-YAPS127A mice developed squamous cell carcinomas (SCC). Although KRT14-E6/E7 mice (only expressing E6/E7) rarely developed CVC after induction with Dox for 12 months, KRT14-E6/E7-YAPS127A mice developed cervical cancer within 4 months of Dox induction. Compared to KRT14-YAPS127A mice, cancer cells in the cervical tissue of KRT14-E6/E7-YAPS127A mice were more proliferative and invasive. Mechanistic studies showed that ectopic expression of YAPS127A in human cervical epithelial cells resulted in a significant increase in cell susceptibility to HPV infection, while inhibition of YAP1 activity reduced the acceptability of cervical epithelial cells to HPV infection. Intriguingly, we found that activation of YAP induced up-regulation of the putative HPV cellular receptor and disrupted innate immunity in cervical epithelial cells. Conclusion: Our research demonstrates that constitutive activation of YAP1 is sufficient to induce cervical SCC. Hyper-activation of YAP increases the susceptibility of cervical epithelial cells to HPV infection. HPV, in turn, synergistically promotes YAP1-induced initiation and progression of cervical cancer. The Hippo/YAP signaling pathway may represent a promising target for developing novel strategies to prevent and treat cervical cancer. [C.H., X.L., and C.H. contributed equally to this work.] Citation Format: Chunbo He, Xiangmin Lv, Cong Huang, Guohua Hua, Jin Zhou, Zhengfeng Wang, Jixin Dong, Peter C Angeletti, Paul F. Lambert, Bo R Rueda, John S Davis, Cheng Wang. Yes-associated protein 1 regulates cervical cancer initiation and progression via suppressing innate immunity and increasing cell susceptibility to human papillomavirus infection [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A01.

Detection of novel Betapapillomaviruses and Gammapapillomaviruses in eyebrow hair follicles using a single-tube 'hanging droplet' PCR assay with modified pan-PV CODEHOP primers.

A modified pan-PV consensus-degenerate hybrid oligonucleotide primer (CODEHOP) PCR was developed for generic and sensitive detection of a broad-spectrum of human papillomaviruses (HPVs) infecting the cutaneous epithelium. To test the analytical sensitivity of the assay we examined 149 eyebrow hair follicle specimens from immunocompetent male patients. HPV DNA was detected in 60 % (89/149) of analysed eyebrow samples with a total of 48 different HPV sequences, representing 21 previously described HPVs and 27 putative novel HPV types. Evidence for ten novel HPV subtypes and seven viral variants, clustering to three out of five genera containing cutaneous HPVs, was also obtained. Thus, we have shown that the modified pan-PV CODEHOP PCR assay is able to identify multiple HPV types, even from different genera, in the same clinical sample. Overall, these results demonstrate that the pan-PV CODEHOP PCR is an excellent tool for screening and identification of novel cutaneous HPVs, even in samples with low viral loads.

Papillomavirus infections in the oral and genital mucosa of asymptomatic women

Human papillomavirus (HPV) has been found in several regions of the body, including the oral cavity. Recently, this virus has been associated with oropharyngeal cancer, but little is known about HPV transmission to the oral cavity. We carried out a study to investigate concurrent oral and cervical infections in 76 asymptomatic women attending a healthcare program. Demographic and behavior data were obtained through a structured questionnaire. Oral and cervical mucosa scrapings were collected and stored for DNA extraction. HPV DNA amplification was performed by polymerase chain reaction assay (PCR) using both primers My09/My11 and FAP59/64, followed by HPV typing with restriction fragment length polymorphism analysis (RFLP) and sequencing. The data collected revealed no risk factors for HPV infection in these 76 women. HPV prevalence of 9.2 and 5.3% was found in cervical and oral mucosa, respectively. Concurrent infections by discordant types were detected in one case only. Sequencing procedures allowed us to detect a new putative HPV 17 subtype from the Betapapillomavirus genus. Our results support the view that cervical and oral HPV infections are independent events. The observed low prevalence of both oral and cervical HPV infections could be associated with attendance in a healthcare program.

Low expression levels of putative HPV encoded microRNAs in cervical samples.

Using small RNA sequencing of libraries established from cervical samples and cervical cancer cell lines, we have previously reported identification of nine and validation of five putative microRNA species encoded by human papillomaviruses (HPV) including five microRNAs encoded by HPV 16. Here we have studied the expression of HPV 16 encoded microRNAs in cervical samples and in HPV 16 containing cell lines. Different sample matrices were collected for the study: 20 paraffin embedded cervical tissue samples, 16 liquid cytology samples, and 16 cervical cell samples from women attending colposcopy due to cervical abnormalities, as well as four HPV 16 containing cell lines. Total RNA was extracted, the samples were spiked with small synthetic control RNAs, and the expression of five HPV 16 encoded microRNAs was assessed by real-time PCR amplification. HPV encoded microRNAs could be frequently detected, albeit at high cycle counts. HPV16-miR-H1 was detected in 3.6 %, HPV16-miR-H3 in 23.6 %, HPV16-miR-H5 in 7.3 %, and HPV16-miR-H6 in 18.2 % of all valid samples. True positive signals for HPV16-miR-H2 could not be detected in any of the samples. Viral microRNAs were detected most frequently in paraffin-embedded samples: in one sample representing normal squamous epithelium, in one cervical intraepithelial neoplasia (CIN) grade 1, one CIN2, three CIN3, two squamous cell carcinoma, three adenocarcinoma in situ, and two adenocarcinoma samples. One liquid cytology sample from a patient with CIN3 as well as all four cell lines were positive for HPV16-miR-H3. In all cases HPV encoded microRNAs were expressed at low levels.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3524-3) contains supplementary material, which is available to authorized users.

Does human papillomavirus-negative condylomata exist?

Condylomata acuminata is caused by human papillomavirus (HPV). PCR with consensus primers will typically detect HPV in >96% of condylomata. Metagenomic sequencing has found that some “HPV-negative” condylomata do indeed contain HPV. We wished to perform a renewed evaluation of the “HPV-negative” condylomata using deeper metagenomics sequencing.Sequencing of whole genome amplified DNA from 40 apparently “HPV-negative” condylomata detected HPV in 37/40 specimens. We found 75 different HPV types, out of which 43 represented novel putative HPV types. Three types were cloned and established as HPV types 200, 201 and 202. Molluscum contagiosum virus was detected in 24 of the 40 samples.In summary, deep sequencing enables detection of HPV in almost all condylomata. “HPV-negative” condylomata might largely be explained by clinical misdiagnosis or the presence of viral variants, distantly related HPV types and/or low viral loads.

Deep sequencing extends the diversity of human papillomaviruses in human skin.

Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.

Fascin and cyclin D1 immunoreactivity in non-neoplastic vulvar squamous epithelium, vulvar intraepithelial neoplasia and invasive squamous carcinoma: correlation with Ki67 and p16 protein expression

AimsTo investigate cyclin D1 and fascin immunoreactivity in normal, reactive and neoplastic vulvar skin correlating the findings with p16 protein and Ki67 expression.Methods66 vulvar biopsy or resection specimens demonstrating normal...

Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.

The Nasal Mucosa Contains a Large Spectrum of Human Papillomavirus Types from the Betapapillomavirus and Gammapapillomavirus Genera

Human papillomavirus (HPV) types from the Betapapillomavirus and Gammapapillomavirus genera are common at cutaneous sites. The aim of this study was to analyze the prevalence of these HPV types in oral and nasal samples. Nasal samples and oral samples were obtained from 312 volunteer Danish healthcare staff (240 women and 72 men), among whom the mean age was 42 years. A total of 311 oral samples and 304 nasal samples were eligible for HPV DNA analysis. HPV types were detected by use of polymerase chain reactions with modified general primers (MGP) and Forslund-Antonsson primers (FAP) and identified by Luminex (for types detected by MGP PCR) or direct sequencing or cloning before sequencing (for types detected by FAP PCR). HPV DNA was detected in 6% of the oral samples and 50% of the nasal samples. Seventy-five diverse HPV types or putative HPV types were identified. HPV types within the Alphapapillomavirus, Betapapillomavirus, and Gammapapillomavirus genera were detected in 3%, 31%, and 23% of the nasal samples, respectively. A putative subtype of HPV76, originally isolated from a feline oral squamous cell carcinoma, was detected in 7 nasal samples. A large spectrum of HPV types from Betapapillomavirus and Gammapapillomavirus have tropism for the nasal mucosa. The implication of the relatively high prevalence of these viruses in the nasal mucosa is unknown.

Unbiased Approach for Virus Detection in Skin Lesions

To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.

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

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.