Type-specific Agreement Research Articles

Field experience with the 8-HPV-type oncoprotein test for cervical cancer screening among HPV-positive women living with and without HIV in LMICs.

Overexpression of HPV-oncoproteins E6 and E7 is necessary for HPV-driven cervical carcinogenesis. Hence, these oncoproteins are promising disease-specific biomarkers. We assessed the technical and operational characteristics of the 8-HPV-type OncoE6/E7 Cervical Test in different laboratories using cervical samples from HPV-positive women living with (WLWH) and without HIV. The 8-HPV-type OncoE6/E7 Test (for short: "OncoE6/E7 test") was performed in 2833 HIV-negative women and 241 WLWH attending multicentric studies in Latin America (ESTAMPA study), and in Africa (CESTA study). Oncoprotein positivity were evaluated at each testing site, according to HIV status as well as type-specific agreement with HPV-DNA results. A feedback questionnaire was given to the operators performing the oncoprotein test to evaluate their impression and acceptability regarding the test. The OncoE6/E7 test revealed a high positivity rate heterogeneity across all testing sites (I2: 95.8%, p < .01) with significant lower positivity in WLWH compared to HIV-negative women (12% vs 25%, p < .01). A similar HPV-type distribution was found between HPV DNA genotyping and oncoprotein testing except for HPV31 and 33 (moderate agreement, k = 0.57). Twenty-one laboratory technicians were trained on oncoprotein testing. Despite operators' concerns about the time-consuming procedure and perceived need for moderate laboratory experience, they reported the OncoE6/E7 test as easy to perform and user-friendly for deployment in resource-limited settings. The high positivity rate variability found across studies and subjectivity in test outcome interpretation could potentially results in oncoprotein false positive/negative, and thus the need for further refinements before implementation of the oncoprotein testing in screen-triage-and-treat approaches is warranted.

NanoString Technology for Human Papillomavirus Typing.

High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter® platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 HPV types and the globin gene. We tested residual DNA extracts from epidemiologic specimens and defined samples (HPV plasmids at 10 to 104 copies/reaction) directly (No-PCR) as well as after L1 consensus PCR of 45 (PCR-45) or 15 cycles (PCR-15). Assay and interpretation followed NS recommendations. We evaluated analytic performance by comparing NanoString results for types included in prior assays: Roche Linear Array (LA) or HPV TypeSeq assay. No-PCR results on 40 samples showed good type-specific agreement with LA (k = 0.621) but sensitivity was 65% with lower limit of detection (LOD) at 104 plasmid copies. PCR-45 results showed almost perfect type-specific agreement with LA (k = 0.862), 82% sensitivity and LOD at 10 copies. PCR-15 results on 75 samples showed substantial type-specific agreement with LA (k = 0.796, 92% sensitivity) and TypeSeq (k = 0.777, 87% sensitivity), and LOD at 10 copies of plasmids. This proof-of-principle study demonstrates the efficacy of the NS platform with HPV CodeSet for type-specific detection using a low number of PCR cycles (PCR-15). Studies are in progress to evaluate assay reproducibility and analytic validation with a larger number of samples.

Extended HPV Genotyping to Compare HPV Type Distribution in Self- and Provider-Collected Samples for Cervical Cancer Screening.

Primary high-risk human papillomavirus (hr-HPV) testing of self-collected cervico-vaginal swabs could increase cervical cancer screening coverage, although triage strategies are needed to reduce unnecessary colposcopies. We evaluated the use of extended hr-HPV genotyping of self-collected samples for cervical cancer screening. We recruited women ages 25-65 years at two colposcopy clinics in North Carolina between November 2016 and January 2019, and obtained self-collected cervico-vaginal samples, provider-collected cervical samples, and cervical biopsies from all enrolled women. Self- and provider-collected samples were tested for 14 hr-HPV genotypes using the Onclarity Assay (Becton Dickinson). We calculated hr-HPV genotype-specific prevalence and assessed agreement between results in self- and provider-collected samples. We ranked the hr-HPV genotypes according to their positive predictive value (PPV) for the detection of cervical intraepithelial neoplasia (CIN) grade 2 or higher (CIN2+). A total of 314 women participated (median age, 36 years); 85 women (27%) had CIN2+. More women tested positive for any hr-HPV on self-collected (76%) than on provider-collected samples (70%; P = 0.009) with type-specific agreement ranging from substantial to almost perfect. HPV-16 was the most common genotype in self-collected (27%) and provider-collected samples (20%), and HPV-16 prevalence was higher in self- than provider-collected samples (P < 0.001). In self- and provider-collected samples, HPV-16 had the highest PPV for CIN2+ detection. Overall sensitivity for CIN2+ detection was similar for both sample types, but the higher HPV-16 prevalence in self-collected samples could result in increased colposcopy referral rates. Additional molecular markers might be helpful to improve the triage of women who are hr-HPV positive on self-collected samples.

Performance of HPV E6/E7 mRNA Genotyping Test on Paired Cervical Cancer Exfoliated Cells and Formalin Fixed Paraffin Embedded Tissues

Investigation of human papillomavirus (HPV) in archival formalin-fixed paraffin-embedded (FFPE) material is important for understanding cervical carcinogenesis. The objective of the present study was to identify the high risk HPVs (HR-HPVs) using HPV E6/E7 mRNA testing from archival tissues in cervical cancer and the relation to HR-HPVs genotypes in paired cervical exfoliated cells. HPV E6/E7 mRNA testing and DNA chip testing were performed in 79 paired cervical FFPE tissues and exfoliated cells from women with histologically confirmed squamous cell carcinoma and adenocarcinoma. Overall agreement in HR-HPVs detection from FFPE samples and cytology samples were 98.5% in HPV 16, 100% in HPV 18, HPV 31, HPV 33, HPV 58, HPV 66, and HPV 68. Type-specific agreement between FFPE samples and cytology samples was 89.1% in HPV positive, 93.5% in HPV 16 and more than 70% in the other HR-HPVs. In conclusion, HR-HPVs were reliably detected in paired FFPE and cytology samples with some variation in type-specific detection.

Primary resistance to Hepatitis B Virus in the treatment-naive Patients

No: 1714 Presentation at ESCV 2015: Poster 2 Primary resistance to Hepatitis B Virus in the treatment-naive Patients M. Altindis1,∗, L. Demir1, I. Uslan2, Ozdemir Mehmet3, M. Baykan3, M. Kosecik4 1 Sakarya University School of Medicine, Dept of Clinical Microbiology, Sakarya, Turkey 2 Sakarya University School of Medicine, Dept of Gastroenterology, Sakarya, Turkey 3 Necmettin Erbakan Uni School of Medicine, Dept of clinical Microbiology, Konya, Turkey 4 Sakarya University School of Medicine, Dept of Pediatry, Sakarya, Turkey Background:Resistance to nucleos(t)ide analogues (NUC) is the main cause of NUC treatment failures leading to disease aggravation and complications. Our aim was to assess the prevalence of primary resistance to NUCs in a large cohort of treatment-naive patients infected with HBV by means of a highly sensitive method for the detection of minority viral populations. Methods: In this study, presence of resistance mutations in treatmentnaive individuals with chronic hepatitis B (CHB) was investigated in Sakarya University Hospital. A total of 59 patients (24 female, 35 male; age range: 19–66 years) diagnosed as CHB were enrolled in the study with informed consent from Gastroenterology, Sakarya anD Konya. All of the patients were negative for hepatitis C andD viruses and human immunodeficiency virus coinfections, and none had a history of interferon or NA treatment. HBV viral load(Montania® 4896, Bosphore® HBV Quantification Kit, Anatolia), HBV markers and hepatic enzymes in patients were determined via standardized commercial assays. For the detection of NA resistance mutations, a partial sequence of approximately 250 nucleotides, harboring the frequently-observed sites for NA resistance was amplified via nested PCR and characterized by direct sequencing of the amplicons(Bosphore® HBV Drug ResistanceMutation Sequencing Kit, Anatolia and Beckman Coulter CEQ 8000 Genetic Analysis System). The sequences were handled and interpreted for the presence ofmutations via various softwares and a web-based virtual phenotyping tool(CEQ 8000 Genetic Analysis System Version 9). Results: All circulating HBV strains were observed as genotype D(D1, D2, D3). At baseline, 59 patients harbored HBV resistanceassociated variants (RAV), generally in low proportions (0.3–20%). 26.9%, 9.7%, 1.6%, 1.6% of the patients displayed RAVs representing less than 1%, 1–5%, 5–10%, 10–20% of the viral quasispecies, respectively. 3 patients harbored RAVs that represented more than 20% of the quasispecies, including rtq215s, rtl91 and rtQ149K variant at 25%. None of the patients were found to harbor variants with both resistance and fitness mutations, which are generally selected on treatment at the sensitivity level of the technique. Conclusions: Primary HBV resistance to NUCs is frequent in treatment-naivepatients. These results further emphasize theneed for using first-line therapies including NUCs with a high barrier to resistance. http://dx.doi.org/10.1016/j.jcv.2015.07.273 Abstract No: 1725 Presentation at ESCV 2015: Poster 2 Development of an automated extraction system for Formalin-Fixed Paraffin Embedded (FFPE) tissue for the downstream detection of Human Papillomavirus (HPV) D. Guerendiain ∗, C. Moore, K. Cuschieri SHPVRL, NHS Lothian, Edinburgh, UK Background: Characterisation of FFPE biopsy material for HPV status is important for both epidemiological purposes and increasingly, for annotation of oropharyngeal squamous cell cancer (OPSCC). While manual extraction procedures for this application have been published–there is a lack of data on the development and performance of automated systems. The objective of this study was to develop and evaluate an automated extraction system for the detection of HPV nucleic acid using the NucliSENS® easyMAG®. Methods: A total of 60 samples were assessed: 30 FFPE sections related to high grade cervical intraepithelial neoplasia (CIN) lesions and 30 sections were derived from OPSCC. All samples had been extracted previously with manual silica columns (QIAamp DNA Mini Kit) and tested with the Optiplex HPV DNA assay (Diamex). Curled sections were obtained from each block with10 m thickness. Sampleswere extracted using the easyMAG® using a protocol adapted for FFPE material. DNA was tested using the Nanodrop® to evaluate the quantity and purity of DNA extracted. Agreement between the original HPV result associated with the manual extract and the results associatedwith the automated extract were assessed. Results: Nucleic acid yields ranged from 4.8 to 88ng/ l on extractsobtained fromtheeasyMAG® platform.At leastpartial concordance was observed in 93% in both cervical and OPSCC samples with an overall Kappa for HPV detection in the total sample (n=60) of 0.8049 (95% CI: 0.62–0.98). Specific kappas on HPV type-specific agreement will be presented. Conclusion:Our results indicate a high agreement between the easyMAG® and theQIAampDNAMiniKit® for the extractionofHPV DNA in FFPE samples derived from the oropharynx and the cervix This extraction method will reduce hands-on time – particularly for batch extraction. http://dx.doi.org/10.1016/j.jcv.2015.07.274

Comparison of the detection of HPV-16, 18, 31, 33, and 45 by type-specific DNA- and E6/E7 mRNA-based assays of HPV DNA positive women with abnormal Pap smears

This study compares the type-specific human papillomavirus (HPV) DNA test with E6/E7 mRNA detection assay because of their importance in cervical cancer screening programs. A total of 105 women with positive high-risk Hybrid Capture 2 or Abbott RealTime High Risk HPV screening test and an abnormal cervical Pap smear were enrolled in the study. HPV typing was performed by multiplex real-time PCR (HPV High Risk Typing Real-TM test). HPV-16, 18, 31, 33, and 45 E6/E7 mRNAs were determined by type-specific real-time NASBA assay (NucliSENS EasyQ® HPV v1.1). Infections caused by HPV-16, 18, 31, 33, and 45 types increased with severity of cervical cytology (p=0.008). Global positivity of five HPV E6/E7 mRNAs was lower than DNA positivity within women with atypical squamous cells of undetermined significance (p=0.016; p=0.008). High agreement of the tests was found in the groups of women with low-grade (p=1.000; p=0.063) and high-grade squamous intraepithelial lesion (p=0.250; p=0.125). Type-specific agreement of both diagnostic approaches was high regardless of cytology. Based on the found differences between HPV-16, 18, 31, 33, and 45 E6/E7 mRNA and DNA positivity, further study is needed to test the role of mRNA testing in the triage of women with atypical squamous cells of undetermined significance in Pap smear.

Brush-based self-sampling in combination with GP5+/6+-PCR-based hrHPV testing: High concordance with physician-taken cervical scrapes for HPV genotyping and detection of high-grade CIN

BackgroundStudies have shown that self-sampling for hrHPV testing (HPV self-sampling) is highly acceptable to women, increases screening participation rate, and may therefore further reduce cervical cancer incidence. However, it is important to clinically validate HPV self-sampling procedures for screening purposes. ObjectivesClinical validation of combined brush-based self-sampling with GP5+/6+-PCR EIA for primary cervical screening. In addition, HPV type-specific agreement between sample types and acceptability of brush-based self-sampling were evaluated. Study design135 women referred for colposcopy took a self-sample at home prior to vaginal- and cervical sampling by a gynaecologist. All women were biopsied for histology. HPV testing was done by GP5+/6+-PCR EIA, with genotyping by reverse line blotting (RLB). Acceptability of sampling methods was measured with a questionnaire. ResultsIn this outpatient population, hrHPV test results showed good concordance between self-samples and physician-taken cervical scrapes (86%, k=0.70), with sensitivities and specificities for CIN2+ that did not differ significantly (93% and 51%, 91% and 51%, respectively (P=1.0)). The clinical sensitivity of brush-based self-sampling combined with GP5+/6+-PCR EIA hrHPV testing for detection of CIN2+ was non-inferior to that of hrHPV testing on physician-taken cervical samples (P=0.018). In addition, hrHPV genotyping results were highly concordant between sample types, with almost perfect agreement for HPV16 (k=0.81) and HPV18 (k=0.92). Finally, 91% of participants described brush-based self-sampling as easy-to-use. ConclusionsBrush-based self-sampling in combination with GP5+/6+-PCR EIA hrHPV testing is acceptable to women and valid for assessing the risk of CIN2+ in comparison to hrHPV testing on physician-taken scrapes. In addition, there was high concordance of HPV genotyping results. Therefore, this HPV self-sampling procedure may be considered for use in routine cervical screening.

Development and Evaluation of a Liquid Bead Microarray Assay for Genotyping Genital Human Papillomaviruses

We developed a liquid bead microarray (LBMA) assay for genotyping genital human papillomaviruses (HPVs) based on the MY09-MY11-HMB01 PCR system and the reverse line blot (RLB) assay probe sequences. Using individual HPV plasmids, we were able to detect as few as 50 copies per reaction. In two separate retrospective studies, the LBMA assay was compared to the RLB assay and to the Hybrid Capture II (hc2) assay. Testing was performed without knowledge of other assay results. In the first study, 614 cervical swab samples (enriched for HPV infection) from 160 young women were tested for HPV DNA, and 360 (74.8%) type-specific HPV infections were detected by both assays, 71 (14.8%) by the LBMA assay only, and 50 (10.4%) by the RLB assay only. Type-specific agreement for the two assays was excellent (99.1%; kappa=0.85; 95% confidence interval [95% CI], 0.82 to 0.88). Samples with discrepant LBMA and RLB test results tended to have low viral loads by a quantitative type-specific PCR assay. In the second study, cervical swab samples from 452 women (including 54 women with histologically confirmed cervical-intraepithelial neoplasia grade 2 or worse [>or= CIN2]) were tested initially by the hc2 and subsequently by the LBMA assay. The estimated sensitivities for >or= CIN2 were similar for the LBMA and hc2 assays (98.4% [95% CI, 95.0 to 100%] and 95.6% [95% CI, 89.2 to 100%], respectively). The percentages of negative results among 398 women without >or= CIN2 were similar for the LBMA and hc2 assays (45% and 50%, respectively). The repeat test reproducibility for 100 samples was 99.1% (kappa=0.92; 95% CI, 0.90 to 0.95). We conclude that the new LBMA assay will be useful for clinical and epidemiological research.

Transplacental transmission of Human Papillomavirus

This paper aimed at studying the transplacental transmission of HPV and looking at the epidemiological factors involved in maternal viral infection. The following sampling methods were used: (1) in the pregnant woman, (a) genital; (b) peripheral blood; (2) in the newborn, (a) oral cavity, axillary and inguinal regions; (b) nasopharyngeal aspirate, and (c) cord blood; (3) in the placenta. The HPV DNA was identified using two methods: multiplex PCR of human β-globin and of HPV using the PGMY09 and PGMY11 primers; and nested-PCR, which combines degenerated primers of the E6/E7 regions of the HPV virus, that allowed the identification of genotypes 6/11, 16, 18, 31, 33, 42, 52 and 58. Transplacental transmission was considered when type-specific HPV concordance was found between the mother, the placenta and the newborn or the mother and cord blood. The study included 49 HPV DNA-positive pregnant women at delivery. Twelve placentas (24.5%, n = 12/49) had a positive result for HPV DNA. Eleven newborn were HPV DNA positive in samples from the nasopharyngeal or buccal and body or cord blood. In 5 cases (10.2%, n = 5/49) there was HPV type-specific agreement between genital/placenta/newborn samples. In one case (2%, n = 1/49) there was type specific HPV concordance between genital/cord blood and also suggested transplacental transmission. A positive and significant correlation was observed between transplacental transmission of HPV infection and the maternal variables of immunodepression history (HIV, p = 0.011). In conclusion the study suggests placental infection in 23.3% of the cases studied and transplacental transmission in 12.2%. It is suggested that in future HPV DNA be researched in the normal endometrium of women of reproductive age. The possible consequence of fetal exposure to HPV should be observed.

Clinical Efficacy of Human Papillomavirus DNA Detection in Urine from Patients with Various Cervical Lesions

A considerable number of adult Korean women avoid a Pap smear due to fear and discomfort of the pelvic examination. A reliable but noninvasive and comfortable screening method would considerably increase the participation rate. To evaluate the clinical efficacy of urine-based human papillomavirus (HPV) detection by oligonucleotide microarray, the results of HPV test from matched cervical swab specimens were compared. HPV DNA was detected in 70 of 100 cervical samples. HPV 16 was the most prevalent type (38/70), followed by types 18, 58, 52, 33, 35, 31, and 51. HPV DNA was identified in 47 of 90 urine samples. HPV 16 was the most prevalent type (30/45), followed by types 18, 52, 35, 51, 58, 33, and 56. The HPV detection rates of the cervical swabs increased in accordance with the severity of the cytologic and histologic diagnosis. The type specific agreement of HPV DNA tests between cervical swabs and urine was good in HPV 16 (kappa index=0.64 [95% CI: 0.50-0.79]), 18, 52, and 58 and fair in HPV 33 and 35. We propose that a urine HPV test is a valuable adjunctive method for a conventional Pap smear and can be used in population screening for cervical cancer in countries where it is difficult to obtain colposcopic specimens for cultural or religious reasons.

7 - Non-haematological Effects of Iron Deficiency

This study compares the type-specific human papillomavirus (HPV) DNA test with E6/E7 mRNA detection assay because of their importance in cervical cancer screening programs. A total of 105 women with positive high-risk Hybrid Capture 2 or Abbott RealTime High Risk HPV screening test and an abnormal cervical Pap smear were enrolled in the study. HPV typing was performed by multiplex real-time PCR (HPV High Risk Typing Real-TM test). HPV-16, 18, 31, 33, and 45 E6/E7 mRNAs were determined by type-specific real-time NASBA assay (NucliSENS EasyQ® HPV v1.1). Infections caused by HPV-16, 18, 31, 33, and 45 types increased with severity of cervical cytology (p = 0.008). Global positivity of five HPV E6/E7 mRNAs was lower than DNA positivity within women with atypical squamous cells of undetermined significance (p = 0.016; p = 0.008). High agreement of the tests was found in the groups of women with low-grade (p = 1.000; p = 0.063) and high-grade squamous intraepithelial lesion (p = 0.250; p = 0.125). Type-specific agreement of both diagnostic approaches was high regardless of cytology. Based on the found differences between HPV-16, 18, 31, 33, and 45 E6/E7 mRNA and DNA positivity, further study is needed to test the role of mRNA testing in the triage of women with atypical squamous cells of undetermined significance in Pap smear.