Molecular Diagnostics of Human Papillomavirus

Sexually transmitted human papillomavirus and related sequelae

SUMMARYMore than 40 types of sexually transmitted human papillomavirus (HPV) infect the oropharyngeal and anogenital mucosa-high-risk types are associated with precancerous and cancerous lesions of the cervix, vagina, vulva, penis, anus, and oropharynx, and low-risk types cause non-malignant disease, such as anogenital warts. Though most HPV infections resolve spontaneously, immunodeficiencies may result in persistent infection and increased risk of HPV-related sequelae. The mechanism by which HPV results in malignant transformation is multifaceted, involving interactions with numerous cellular pathways, the host immune system, and potentially the host microbiome. Vaccination against HPV is highly efficacious in the prevention of infection and related sequelae, and there now exist several approved formulations that protect against both high- and low-risk types. Despite the advent of vaccination, early detection and treatment of cervical and anal precancerous lesions continues to be integral to secondary prevention-molecular HPV testing, cytology, and tissue biopsy allow for triaging of patients, after which appropriate treatment with close follow-up can avert cancer development.

An insight into clinical and laboratory detections for screening and diagnosis of cervical cancer

INTRODUCTION

Cervical cancer is the most frequent malignancy among women caused by an unresolved long-term infection with distinct human papillomavirus (HPV) genotypes. It is the fourth most common form of cancer among women worldwide. The two oncogenic genotypes, HPV 16 and 18, are responsible for >70% of all cervical cancers worldwide. Cervical cancer is one of the most successfully preventable and treatable forms of cancer if detected early.

AREAS COVERED

In this review article, we have summarizedsummarised the different approaches used in clinical diagnosis and research laboratories to detect HPV-related changes associated with cervical cancer for a better understanding of the advantages and limitations of these tests.

EXPERT OPINION

Despite the well-known screening strategies for cervical cancer, developing nations lack effective implementation due to various factors. With the current rate of cervical cancer cases, precise and timely identification of HPV can significantly impact the prevention and efficient management of cervical cancer. Cervical cancer is the most common gynecological cancer in developing countries. The primary screening test with cytology and molecular testing of HPV is important for preventing cervical cancer. To address these issues, several point-of-care assays have been developed to facilitate rapid screening of HPV with the least turnaround time.

High yield gold nanoparticle-based DNA isolation method for human papillomaviruses genotypes from cervical cancer tissue samples

Gold nanoparticles (AuNPs) are commonly used in biosensors of various kinds. However, its application to extract DNA from cancer tissues has not been extensively studied. The purification of DNA from cancer tissues is an important step in diagnostic and therapeutic development. Almost, all cervical cancer cases are associated with high-risk human papillomavirus (HR-HPV) infection. Accurate viral diagnosis has so far relied on the extraction of adequate amounts of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. Till now, no specific and sensitive DNA purification method has been introduced for the extraction of HR-HPV from FFPE tissue. Since the commercially available purification kits are not sensitive and specific enough for HR-HPV DNA targets, in this study, a DNA purification method was designed based on AuNPs to purify sufficient amounts of HR-HPV DNA from cervical cancer tissue samples. AuNPs were coated with a series of oligonucleotide probes to hybridize to specific DNA sequences of HR-HPV genotypes. Results showed that 733 out of 800 copies of type-specific HPV DNA were recovered with complete specificity, compared to 36 copies with a standard commercial kit (Qiagen FFPE). The high yield of DNA (91.6%) is the main advantage of the AuNPs-probe purification method.

Detection of human papillomavirus in oropharyngeal squamous cell carcinoma

Worldwide there has been a significant increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) etiologically attributed to oncogenic human papillomavirus (HPV). Reliable and accurate identification and detection tools are important as the incidence of HPV-related cancer is on the rise. Several HPV detection methods for OPSCC have been developed and each has its own advantages and disadvantages in regard to sensitivity, specificity, and technical difficulty. This review summarizes our current knowledge of molecular methods for detecting HPV in OPSCC, including HPV DNA/RNA polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), p16 immunohistochemistry (IHC), and DNA/RNA in situ hybridization (ISH) assays. This summary may facilitate the selection of a suitable method for detecting HPV infection, and therefore may help in the early diagnosis of HPV-related carcinoma to reduce its mortality, incidence, and morbidity.

Human Papillomavirus Genome based Detection and Typing: A Holistic Molecular Approach

Human Papillomavirus (HPV) is a species specific double-stranded DNA virus infecting human cutaneous or mucosal tissues. The genome structure of HPV is extremely polymorphic hence making it difficult to discriminate between them. HPV exhibits numerous dissimilar types that can be subdivided into high-risk (HR), probably high-risk and low-risk (LR), causing numerous types of cancers and warts around the genital organs in humans. Several screening methods are performed in order to detect cytological abnormalities and presence or absence of HPV genome. Currently available commercial kits and methods are designed to detect only a few HR/LR-HPV types, which are expensive adding to the economic burden of the affected individual and are not freely available. These gaps could be minimized through Polymerase Chain reaction (PCR) method, which is a gold standard and a cost-effective technique for the detection of most HPV (both known and unknown) types by using specific consensus primers in minimal lab setup. In this context, numerous studies have validated the effectiveness of different sets of consensus primers in the screening of HPVs. Numerous consensus primers, such as E6, E6/E7, GP-E6/E7, MY09/11, GP5+/GP6+, SPF10, and PGMY09/11 have been developed to detect the presence of HPV DNA. In addition, HPV detection sensitivity could be achieved through consensus primer sets targeting specific ORF regions like L1 and E6, which may finally assist in better diagnosis of several unknown HR-HPVs. The present review, provides a summary of the available methods, kits and consensus primer sets for HPV genome based detection, their advantages and limitations along with future goals to be set for HPV detection.

Amplification chemistries in clinical virology

Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.

Prevention of cervical cancer development through early detection of HPV using novelty molecular applications

Human Papillomavirus (HPV) is the predominant cause of cervical cancer worldwide. The infections with HPVs 16 and 18 have a high oncogenic risk for cancer development. Besides, the genes E6 and E7 encode viral oncoproteins associated with infection. New molecular techniques for HPV detection, show important advantages such as high sensitivity, recognition capacity, reliability, among others. These techniques allow the standardization of new protocols associated with the detection in a variety of substances and samples. The stretch relationship between the virus and the disease open a new field to study early detection of the HPV infection. Additionally, less concentration of the sample is needed. Considering the significance of the detection, the present paper explains five novelty molecular applications for the prevention cervical cancer and early detection of HPV such as RNA in situ Hybridization for the detection of HPV E6/E7, genosensors, electrochemical DNA biosensor, PCR-based urine assay and a semen assay for detection of HPV. All the methods related to DNA samples could be used for both genders, there are more acceptable and easy to collect.

Genotypes distribution of human papillomavirus in cervical samples of Ecuadorian women

INTRODUCTION

Human papillomavirus (HPV) is considered a necessary causative agent for developing oropharyngeal, anal and cervical cancer. Among women in Ecuadorian population, cervical cancer ranks as the second most common gynecological cancer. Not many studies about HPV burden have been published in Ecuador, and genotypes distribution has not been established yet. The little data available suggest the presence of other genotypes different than 16 and 18.

OBJECTIVES

In the present study, we attempt to estimate the prevalence of HPV 16, HPV 18 and other 35 genotypes among Ecuadorian women undergoing cervical cancer screening. The overall prevalence of HPV infection was also estimated.

METHODS

Routine cervical samples were analyzed using Linear Array(r) HPV Genotyping test (Roche).

RESULTS

A total of 1,581 cervical samples obtained from Ecuadorian women undergoing cervical cancer screening were included in this study. HPV DNA was detected in 689 cervical samples (43.58%). Of these samples, 604 (38.20%) were positive for a single HPV genotype, while another 85 (5.37%) samples were positive for multiple HPV types. Genotype 16 (5.50%) resulted in the most frequently detected type in both single and multiple infections. HPV 33 (4.55%) and HPV 11 (3.80%) occupied the second and the third place in frequency among all detected genotypes.

CONCLUSIONS

Viral genotypes different from HPV 16 and HPV 18 are frequently detected among Ecuadorian women. The overall prevalence of HPV resulted higher than the one reported in other South American countries with a greater burden in the second and third decades of life.

Comparison of GeneFinder human papillomavirus (HPV) Liquid Beads Microarray PCR Kit and Hybrid Capture 2 Assay for Detection of HPV Infection

BACKGROUND

Along with advances in methodological technologies, various assays for detecting high-risk human papillomavirus (HR HPV) have been introduced. The GeneFinder HPV liquid beads microarray PCR kit is one of the recently developed. Our aim was to compare the performance of GeneFinder to Hybrid Capture 2 for detection of HR HPV.

METHODS

A total of 900 cervical swab specimens were obtained. All specimens were submitted for HR HPV detection with Hybrid Capture 2 (HC2) and GeneFinder and then additionally analyzed the discordant or both positive results using restriction fragment mass polymorphism (RFMP) genotyping analysis.

RESULTS

Hybrid Capture 2 detected 12.8% cases and GeneFinder detected 15.8% cases with 13 HR HPV types. Also, GeneFinder detected 27.4% cases for 32 detectable HPV types. The overall agreement rate was 93.2% with 0.724 kappa coefficient. Discordant results between these two assays were observed in 56 cases. HC2 showed sensitivity of 83.5% and specificity of 95.9%, while GeneFinder showed sensitivity of 85.4% and specificity of 91.9%. For HPV 16 or HPV 18 detection, GeneFinder showed 95.0% or 66.7% of sensitivity and 99.2% or 100%, respectively. Overall coinfection rate was 15.4% (38/247) in GeneFinder analysis.

CONCLUSIONS

Considering the high agreement rate with HC2, high sensitivity and the ability to differentiate 32 HPV genotypes including HPV 16/18, GeneFinder could be used as a laboratory testing method for the screening of HPV infections. The use of GeneFinder may also contribute to future research associated with the significance of various HPV types and multiple coinfections.

Convenient detection of HPV virus in a clinical sample using concurrent rolling circle and junction probe amplifications

Herein we show that two isothermal amplification strategies, rolling circle amplification and junction probe strategy, can be used in tandem in the same tube under isothermal conditions to detect HPV16 in clinical cervical swabs. It was discovered that the prior treatment of the clinical sample with a cocktail of restriction endonucleases (REAses) to digest the genomic DNA facilitated the isothermal detection assay.

Clinical validation of AdvanSure GenoBlot assay as primary screening and test of cure for human papillomavirus infection

Background

Clinical specificity and sensitivity are essential factors in the adoption of a human papillomavirus (HPV) test as a primary screening tool and test of cure after treatment of cervical cancer and precancerous lesions (High-Risk-Lesion). Using histologically-confirmed High-Risk-Lesion-patient specimens with postoperative follow-ups, we performed clinical validation of the AdvanSure GenoBlot Assay (GenoBlot; LG Life Sciences, Korea).

Methods

The study population included 100 cases with High-Risk-Lesion, 96 with high-risk genotype positive and cervical intraepithelial neoplasia (CIN) 1 or better, and 39 with HR-negative and better than CIN 1. Forty-eight High-Risk-Lesion cases received follow-up HPV exams after surgery. For validation as a test of cure, 48 preoperative specimens (PreOP) and 78 postoperative specimens (PostOP) from 48 subjects were separately analyzed. The results of HPV DNA chip tests (HPVDNAChip; BioMedLab Co., Korea) and sequencing were cross-compared.

Results

The concordance rates for each genotype between HPVDNAChip and GenoBlot were between 96.3-100%. The accuracy of HPVDNAChip and GenoBlot was 87.9% and 96.6%, respectively. Genotype-based specificity for High-Risk-Lesion detection was higher than 87% for both assays; genotype 16 showed the highest sensitivity. In the PostOP group, the positive rates for HPVDNAChip and GenoBlot were 30.8% and 47.4%, respectively.

Conclusions

GenoBlot showed a higher positive rate than HPVDNAChip for each genotype, with concordance rate and accuracy being similar to previous reports. As a test of cure, GenoBlot performed better than the HPVDNAChip.