Real-time duplex PCR for simultaneous HPV 16 and HPV 18 DNA quantitation

Prevalence and significance of HPV DNA detection below the clinical threshold of the commercial kit Alinity m HR-HPV assay (Abbott)

The positive clinical threshold of human papillomavirus (HPV) tests validated for primary cervical cancer screening (CCS) is designed to offer an optimal balance between clinical sensitivity and specificity. However, there may be a gap between the analytical sensitivity of the test and the positive clinical threshold, referred to here as the "gray-zone." This study aims to determine the prevalence and significance of HPV results obtained in the gray-zone in routine practice. Cervical samples obtained in our institution for CCS over a 22-month-period were tested with the Alinity m HR-HPV Assay (Abbott). Clinical and biological data, including cytological results and patients' HPV history were collected. Of the 6101 samples collected, 1.7% had an HPV result in the gray-zone (102 patients). The proportion of gray-zone results varied according to HPV genotype, reaching 11.8% of samples with detectable HPV DNA in the case of HPV31/33/52/58 genotypes. Reflex cytologies showed no abnormalities or Atypical Squamous Cells of Undetermined Significance results in 74.6% and 17.9% of cases, respectively. A previous or subsequent HPV-positive result with a (possibly) identical genotype was observed in 58% and 38% of cases, respectively. Two women with a history of persistent HPV detection had a CIN2+ lesion 1 year after the gray-zone result. In conclusion, the proportion of HPV results in the gray-zone varies according to genotype. No cytological abnormality is observed in the majority of cases, but a few rare patients with a history of persistent HPV infection should be closely monitored even if the HPV result is transiently located in the gray-zone.

High levels of HPV16-L1 antibody but not HPV16 DNA load or integration predict oropharyngeal patient outcome: The Papillophar study

The incidence of oropharyngeal cancers (OPC) is increasing in the world. Among OPC, those induced by human papillomaviruses have a better prognosis than non-HPV-associated OPC. The objective of this study was to highlight the relevance of HPV16 load, HPV16 DNA integration and HPV16-L1 serology on progression-free survival and overall survival of OPC patients. The PAPILLOPHAR cohort consists of 362 patients with oropharyngeal squamous cell carcinomas prospectively followed up for 5 years after treatment. Tumor biopsies and sera were collected at inclusion to investigate tumor HPV DNA/RNA characteristics and HPV16 L1 serology, respectively. Twenty-seven percent of tumor biopsies were HPV DNA- and RNA-positive and HPV16 represented 93% of HPV-positive cases. Among them, neither HPV16 viral load nor HPV16 DNA integration was associated with overall survival (OS) or progression-free survival (PFS). In contrast, high anti-HPV16 L1 antibody titers were significantly associated with a better OS and PFS. This study reveals that HPV16 load and integration are not relevant prognosis biomarkers in OPC patients.Clinical Relevance: High levels of HPV16 L1 antibodies may be useful to predict OPC patient outcome following treatment.ClinicalTrials.gov Identifier: NCT00918710, May 2017.

Longitudinal follow-up of HPV16 sequence after cervical infection: Low intrahost variation and no correlation with clinical evolution

Human papillomavirus (HPV) 16 exhibits different variants that may differ in their carcinogenic risk. To identify some high-risk variants, we sequenced and compared HPV16 whole genomes obtained from a longitudinal cohort of 34 HPV16-infected women who had either spontaneously cleared their infection (clearance group or "C"), or developed cervical high-grade lesions following a viral persistence (group persistence or "P"). Phylogenetic analysis of paired samples obtained at the beginning (C0 or P0) and at the end (C2 or P2) of the follow-up (median intervals between C0-C2 and between P0-P2 were 16 and 36.5 months, respectively) revealed a low genetic variability within the host compared to the genetic interhost diversity. By comparing our HPV16 sequences to a reference sequence, we observed 301 different substitutions, more often transitions (60.9%) than transversions (39.1%), that occurred throughout the viral genome, but with a low frequency in E6 and E7 oncogenes (10 and 9 substitutions), suggesting a high conservation of these genes. Deletions and insertions were mostly observed in intergenic regions of the virus. The only significant substitution found between the subgroups C2 and P2 was observed in the L2 gene (L330F), with an unclear biological relevance. Our results suggest a low longitudinal intrahost evolution of HPV16 sequences and no correlation between genetic variations and clinical evolution.

Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses

Simple and standardized approaches for genome analysis of human papillomavirus (HPV) by next-generation sequencing are needed. The aim of the study was to develop a protocol for direct deep sequencing of high-risk (hr) HPV strains, based on the widely used commercial Hybrid Capture 2 (QIAGEN) test, without any additional probe design. This protocol was applied to 15 HPV-positive and two HPV-negative cervical samples or cell lines and validated at the genotype level by comparing the sequencing results to those obtained using a commercial genotyping kit. The performance of our protocol, presented in this proof-of-principle study, supports its use for accurate characterization of genetic variants of hrHPV.

HPV16 Load Is a Potential Biomarker to Predict Risk of High-Grade Cervical Lesions in High-Risk HPV-Infected Women: A Large Longitudinal French Hospital-Based Cohort Study

Simple Summary

This study aimed at assessing HPV16 and HPV18 viral loads to predict the development of cervical high-grade lesion. Among 885 women positive for hrHPV and presenting no or mild cytological abnormalities, HPV16 and HPV18 prevalence was 25.9% and 8.4%, respectively. Of those women, 135 developed a high-grade lesion during the follow-up. Considering an HPV16 viral load cut-off set at 3.2 log₁₀ GE/10³ cells a subgroup of women at high risk of developing high-grade cervical lesion (HR = 2.67; 95% CI 1.80–3.97 p ≤ 0.0001) has been identified. Moreover, a composite score based on HPV16 load, cytology and hrHPV detection allowed for CIN2+ risk stratification. To conclude, HPV16 load is a relevant biomarker to identify women at high risk for developing precancerous lesions of the cervix.

Abstract

High-risk HPV (hrHPV) testing has been implemented as a primary screening tool for cervical cancer in numerous countries. However, there is still a need for relevant triage strategies to manage hrHPV positive women to avoid excessive referral to colposcopy. The objective of this study was to assess, in women infected by hrHPV and presenting no or mild cytological abnormalities, HPV16 and HPV18 viral loads to predict the development of cervical high-grade lesion. Among 2102 women positive for hrHPV, 885 had no lesion or mild cytological abnormalities at baseline and had at least one follow-up (FU) visit. HPV16 and HPV18 prevalence was 25.9% and 8.4%, respectively. Of those women, 15% developed a high-grade lesion during the FU. An HPV16 viral load cut-off set at 3.2 log₁₀GE/10³ cells permitted to identify a subgroup of women at high risk of developing high-grade cervical lesion (HR = 2.67; 95% CI 1.80–3.97; p ≤ 0.0001). No specific HPV18 viral load threshold could have been defined in regard to the present study. In multivariate analysis, HPV16 load (absence/log₁₀GE/10³ cells < 3.2 vs. ≥3.2), RLU/PC 239 (1–100 pg/mL vs. >100 pg/mL) and cytology (normal vs abnormal) were independently associated with a significant increased risk of high-grade lesion development and were used to construct the prognostic score. In conclusion, HPV16 load is a relevant biomarker to identify women at high risk for developing cervical precancerous lesions.

Successful retrieval of human papillomavirus DNA after a 4.5 year storage on FTA elute cards

Efficient primary (vaccination) and secondary (screening) prevention strategies have the potential to eliminate cervical cancer worldwide. In this context, surveillance of HPV infections remains mandatory to assess the efficacy and the impact of screening and vaccination policies. Therefore there is a need to safely store cervical samples to conduct long-term studies in vaccinated and non-vaccinated subjects. Up-dated data on cervical specimen preservation on FTA® cards indicate that HPV DNA can be safely retrieved after 54 months of storage. A concordance of 97 % was achieved between HPV genotypes detected in initial cervical samples and on FTA® cards 4.5 years later. Even if a drop in HPV viral loads was observed in some cases at 4.5 years, using FTA® cards for safe and long-term storage of cervical samples represents an interesting option.

Development and interlaboratory agreement of real-time PCR for HPV16 quantification in liquid-based cervical samples

High risk HPV infection is the necessary cause for the development of precancerous and cancerous lesions of the cervix. Among HPV, HPV16 represents the most carcinogenic type. Since the determination of HPV16 DNA load could be clinically useful, we assessed quantitative real-time PCR targeting E6HPV16 and albumin genes on two different platforms. Series of SiHa cells diluted in PreservCyt were used to assess repeatability and reproducibility of two in-house real-time PCR techniques run in two different laboratories to determine HPV16 load. Furthermore, 97 HPV16 positive cervical samples were evaluated to estimate inter-center variability using Bland-Alman plots. As a whole, both techniques presented coefficients of variation for HPV16 load measurement similar to those established for other virus quantification with commercial kits. Moreover, the two real-time PCR techniques showed a very good agreement for HPV16 load calculation. Finally, we emphasize that robust HPV16 DNA quantification requires normalization of viral load by the cell number.

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HPV16 viral load could be a useful biomarker for the management of HPV positive women.

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Coefficient of variation for HPV16 viral load ranged from 7% to 62%.

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HPV16 viral load quantification requires normalization by the cell number.

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HPV16 viral load precision increases with the use of an internal calibrator.

Human papillomaviruses in colorectal cancers: A case-control study in western patients

BACKGROUND

Colorectal cancer (CRC) is one of the most common cancers. As in other cancer locations, the involvement of human papillomaviruses (HPV) has been suggested but remains highly debated with wide differences among reported prevalence of HPV infection in CRCs.

AIM

To determine the actual prevalence of high risk HPV16 and 18 in a large case-control study.

METHODS

CRC specimens were used for analysis of both tumor and distant healthy tissue. As a non-malignant control group, samples from sigmoid diverticulosis resections were studied. Detection of HPV16 and HPV18 DNA was performed using a real time polymerase chain reaction (qPCR). Ten percent of tumor samples were also randomly subjected to a complete HPV genotyping using the INNO-LiPA technique.

RESULTS

467 samples were analyzed: 217 tumor samples from 210 CRCs, 210 distant healthy tissue samples, and 40 sigmoid samples. HPV18 DNA was never amplified and HPV16 was amplified only three times in tumor tissues with viral loads under or at the limit of quantification. New extraction from the same tumor blocks for these samples revealed no HPV with qPCR and INNO-Lipa assays.

CONCLUSION

With adequate procedures and reliable techniques, no HPV was detected in the largest case-control study so far, bringing more evidence on the absence of involvement of HPV in CRCs.

[Molecular diagnosis of human papillomaviruses (HPV): What test(s) in clinical practice?]

Prescription of an HPV test in practice will enable the clinician to optimize the monitoring and the management of patients, especially in the context of cervical cancer screening. Numerous HPV tests are available that present different analytical and clinical sensitivity and specificity. International recommendations on clinical performance of HPV tests used for cervical cancer screening have been published by a group of experts, and tests that meet these performance criteria should be used. Apart from the HPV detection kit, the whole circuit from sampling to report of the results must be considered. This implies that the pre-analytical (sampling, quality of sample collection medium, storage condition and sample transportation…) and post-analytical steps (quality of result reporting, providing expert advices…) are also standardized. For this purpose, medical-biology laboratories are subjected to a COFRAC certification, as defined by the international standard ISO 15189 providing quality criteria for any clinical laboratory test and HPV test in particular.

High prevalence of abnormal cervical smears in a hospital cohort of French women beyond the upper age limit screening program

OBJECTIVE

To determine the prevalence of cytological abnormalities and high risk Human PapillomaVirus (hrHPV) in cervical smears from French women aged over 65 years who attended the referent Gynecology Clinic of the Besançon University Hospital.

METHODS

Between 2002 and 2012, 796 French women aged 66-99 years were cotested for cytology and hrHPV by Hybrid Capture 2 (hc2). hc2-positive cases were subjected to real time PCR for specific HPV 16/18/45 genotyping. Women with normal Pap smears and positive for hrHPV were followed-up every 12 months.

RESULTS

Cytological abnormalities were detected in more than 30% of women and cervical cancers (CC) in 2.9% of women. Benign lesions were more frequent in women aged 66-75 years while (pre)-malignant lesions were preferentially found in women over 76. The prevalence of hrHPV was 22.7%. HPV 16 was the most frequent (23.8%), followed by HPV 45 (7.7%) and HPV 18 (3.9%). The rate of hrHPV increased with the lesion severity and HPV 16 was identified in 50% of CC. Among the followed-up women, those who developed CIN3 were HPV16 positive at study entry.

CONCLUSION

The study provides important estimates of the prevalence of cervical abnormalities and hrHPV positivity in a French hospital based-population over 65. Findings suggest to consider this high risk population in regards to cervical cancer.

Duplex Real-time PCR assay and SYBR green I melting curve analysis for molecular identification of HPV genotypes 16, 18, 31, 35, 51 and 66

Long-term infection with high-risk HPV genotypes is the leading cause of cervical cancer. In the present study a Duplex Real-time PCR assay was developed in order to identify HPV types 16, 18, 31, 35, 51 and 66 in three reactions, through SYBR green I melting curve analysis. The method utilizes type-specific primer sets that allowed the amplification of highly conserved regions of L1 gene. Reconstitution experiments were conducted by using HPV DNA plasmids in order to determine the sensitivity of the assay. The newly designed assay has a limit of detection of 10 copies per reaction. The most prevalent HPV genotype in single and in multiple HPV infections was HPV16 followed by HPV18, HPV51, HPV31, HPV35 and HPV66. The proposed method is a simple, specific, sensitive and cost-effective assay that can be easily incorporated in small and medium size laboratories for the rapid identification of the most clinically important HPV genotypes.