Journal of Clinical Virology

Assessing sample adequacy and clinical performance of self-collected and clinician-collected HPV specimens using internal control Ct values

Human papillomavirus (HPV) testing is the primary method for cervical cancer screening, but reliable detection depends on adequate sample cellularity. Cycle threshold (Ct) values for the assay's internal control (IC), such as β-globin, are commonly used as proxies for adequacy, yet standardized Ct cut-offs are lacking. We aimed to contribute evidence-based thresholds for sample adequacy using real-world data. We analyzed 237,853 clinician-collected and self-collected samples tested with the BD Onclarity™ HPV Assay between 2022 and 2024. β-globin Ct values were assessed by HPV status to evaluate adequacy. Histologically confirmed CIN2+ outcomes were linked via the National Cervical Screening Registry to assess clinical performance. Among 110,482 clinician-taken samples, 73.63 % (81,350) were HPV negative; 74.32 % (60,457) of these had β-globin Ct ≤28, and only 1.28 % exceeded Ct 32.1. In 127,390 self-collected samples, 83.47 % (106,329) were HPV negative; 99.66 % (105,967) had Ct ≤28 and only 0.06 % exceeded Ct 32.1. HPV positivity declined gradually beyond Ct 26 and more markedly above Ct 28. CIN2+ cases (n = 5546) were rarely HPV negative (n = 73), and these showed low β-globin Ct values, indicating adequate cellularity. Self-collected samples had significantly lower Ct values than clinician-taken ones (median 21.5 vs. 26.5; p < 2.2e-16), likely due to lower resuspension volume. Both clinician- and self-collected samples showed adequate cellularity, with potentially false negative HPV results from low cellular content appearing rare. Observed patterns suggest Ct <26 as optimal and Ct <28 as a minimum for program-level quality assurance with the BD Onclarity™ HPV Assay.

2023 global inventory of commercial molecular tests for human papillomaviruses (HPV)

To suit the needs of the human papillomaviruses (HPV) community comprehensively, a range of commercial HPV tests with different performance characteristics are required. Four periodic inventories of commercial HPV molecular tests present in the global market were published previously in 2010, 2012, 2015 and 2020. For the fifth inventory, data were retrieved from internal files and a detailed search using the main bibliographic databases as well as general internet search without period or language restrictions was performed in December 2023. At least 264 distinct HPV tests (and 511 test variants) were available globally in December 2023. A small 2020-2023 net increase in total numbers was observed, but with a strong introduction/withdrawal dynamic: 86 new distinct HPV tests (and 141 variants) were introduced and 76 tests (and 55 variants) were withdrawn from the market in the last four years. Although quality improvement of some tests was recorded, half of all HPV tests are still without a single peer-reviewed publication, and 79 % of tests are without published evidence that demonstrate performance characteristics are in line with requirements agreed in the HPV community. Only a relatively small pool of tests fulfill the operational/performance characteristics required to meet the global cervical cancer screening challenge. Although clinical and analytical performance characteristics of many commercial HPV tests are largely unknown, such tests are used worldwide in daily clinical practice and research, with potentially deleterious consequences. Due to this long-lasting unfavorable situation, significant scope for improvement persists for both manufacturers of HPV tests and the HPV community.

The Human Papillomavirus (HPV) Laboratory e-Manual: A comprehensive guide for HPV testing and research

Human Papillomavirus (HPV) vaccination and HPV-based cervical cancer screening are central pillars of the World Health Organization (WHO) global cervical cancer elimination strategy. The WHO HPV Laboratory Manual, published in 2009, has provided essential guidance to promote an internationally comparable quality of HPV testing for many years. As the development in this area is rapid, the Global Network of National HPV Reference Laboratories considered that there is a need for an updated HPV Laboratory e-Manual to serve as a comprehensive and interactive resource for professionals engaged in quality-assured HPV testing for research and/or HPV-based cancer control. The HPV Laboratory e-Manual covers key areas, including laboratory quality assurance, HPV taxonomy and risk association, collection and handling of specimens, nucleic acid extraction, HPV detection and typing, HPV serology, data management, and the use of international standards. It provides up-to-date protocols and best practices to enhance accuracy and reliability of HPV testing. Interactive features allow for real-time updates, making it a dynamic resource for laboratories worldwide. The e-Manual is freely available at: https://www.hpvcenter.se/hpv-laboratory-manual/. The e-Manual has been developed by international experts from 11 countries, including contributors from the International HPV Reference Center (IHRC, Sweden), the CDC's Global HPV Reference Laboratory (USA), and multiple National HPV Reference Laboratories (NRLs). The standard procedure for writing a chapter was that 2 NRLs authored the chapter and 1 other NRL reviewed it. The HPV Laboratory e-Manual represents a step toward global harmonization in laboratory methodologies for HPV testing, underpinning both research and cervical cancer control efforts.

IPVS policy statement on HPV nucleic acid testing guidance for those utilising/considering HPV as primary precancer screening: Quality assurance and quality control issues

We advise that only clinically validated HPV assays which have fulfilled internationally accepted performance criteria be used for primary cervical screening. Further, assays should be demonstrated to be fit for purpose in the laboratory in which they will ultimately be performed, and quality materials manuals and frameworks will be helpful in this endeavor. Importantly, there is a fundamental shortage of well validated, low-cost, low complexity HPV tests that have demonstrated utility in a near-patient setting; representing a significant challenge and focus for future development in order to reach the WHO's goal of eliminating cervical cancer.

Clinical accuracy of OncoPredict HPV Quantitative Typing (QT) assay on self-samples

The VALHUDES initiative was established to assess the clinical accuracy of HPV assays to detect cervical precancers using urine and vaginal self-samples compared to cervical clinician-collected samples. Here, the clinical performance of OncoPredict HPV Quantitative Typing (QT) assay (OncoPredict QT) was evaluated. 490 women referred to colposcopy self-collected a urine and a vaginal specimen using Colli-Pee and FLOQSwab, respectively. Subsequently, a colposcopy was performed, and a cervical sample was collected with Cervex-Brush, followed by biopsy if clinically indicated. Vaginal samples were transported dry and resuspended in 5 mL of eNAT medium, whilst cervical brushings were immediately transferred in 20 mL ThinPrep. The clinical sensitivity of OncoPredict HPV QT testing for CIN2+ in urine and vaginal self-samples was similar to cervical samples (ratios of 0.99 [95 % CI 0.94-1.05] and 1.00 [95 % CI 0.96-1.04]), respectively, when manufacturer's cut-offs were applied. The specificity for <CIN2 on both self-samples was lower than on cervical samples (urine/cervical ratio = 0.91 [95 % CI 0.84-0.98]; vaginal/cervical ratio = 0.90 [95 % CI 0.84-0.98]). Cut-off optimisation improved specificity without compromising sensitivity. Median viral load values adjusted for cellularity were significantly higher in cervical samples compared to urine or vaginal self-samples, in general for all 12 high-risk HPV and in particular for HPV16, 18, 31, 33, 35, 45, 51, 58 (p < 0.05). No difference was observed in median viral loads between urine and vaginal samples. Following cut-off optimisation OncoPredict HPV QT assay demonstrated similar accuracy on self-collected versus cervical samples.

Peptide-assisted direct detection of HPV nucleic acids from liquid-based cytology samples without extraction

High-risk human papillomavirus remains the causal agent of nearly all cervical cancers. And we need tools for rapid detection that work in routinely taken samples (e.g., PreservCyt®) that can speed up, facilitate or simplify the extraction process. Conventional workflows rely on nucleic-acid extraction, a cost- and labor-intensive step that restricts scalability in both high-throughput and resource-limited settings. Here, we introduce MDP-1, a rationally designed peptide that represents the prototype of a new class of capsid-targeted diagnostic enhancers. Unlike antimicrobial peptides historically developed for therapeutic membrane lysis, MDP-1 was engineered to bind the HPV L1 major capsid protein, interfere with L1-L1 interactions, and promote partial capsid destabilization to enhance genome accessibility. In silico docking demonstrated favorable binding (HADDOCK score -173.4 ± 6.2; BSA 1958 ± 83.9 Ų; RMSD 1.8 ± 0.1 Å) with extensive electrostatic and hydrophobic complementarity. When integrated into a direct-to-PCR workflow, MDP-1 enabled robust amplification from unextracted PreservCyt® specimens, maintaining efficiencies within 90-110 % and achieving a limit of detection of 1.25 copies/µL. Analytical specificity testing confirmed no cross-reactivity, while interference studies showed tolerance to common clinical inhibitors. In a feasibility cohort (n = 53), the MDP-1 workflow achieved 93.5 % sensitivity (95 % CI: 78.6-99.2) and 99.3 % specificity (95 % CI: 85.4-99.9) for the detection of high-risk HPV DNA, with an overall accuracy of 98.5 % compared to extraction-based qPCR and strongly correlated Ct values (R² = 0.772). This proof-of-concept positions MDP-1 as a first-in-class tool that recasts HPV diagnostics by leveraging peptide-virion interactions to bypass inhibitors and eliminate timely and costly extraction workflows.

Cervical human papillomavirus DNA detection in women living with HIV and HIV-uninfected women living in Limbe, Cameroon

There are limited data on cervical HPV prevalence in Cameroon and none from its Anglophone region. We investigated cervical HPV prevalence in HIV-uninfected (HIV[-]) and HIV-infected (WLWH) women living in the region. A convenience sample of consecutively recruited HIV[-] women (n = 295) and women living with HIV (WLWH) (n = 560) attending the Limbé Regional Hospital were enrolled into a cervical screening study. Women underwent screening that included HPV testing of self-collected and provider-collected specimens. We calculated the HPV prevalence by HIV status, overall and stratified by age, and among WLWH, stratified by CD4 counts. We compared the concordance for the detection of HPV between self- and provider-collected specimens. Crude HPV prevalence was 21.69 % (95 % confidence interval [95 %CI] = 17.21-26.48 %) for HIV[-] women and 46.43 % (95 %CI = 42.24-50.66 %) for WLWH (p < 0.001). Among WLWH, older age (p HIV-related immunosuppression was a risk factor for HPV prevalence in this population. HPV testing of self-collected specimens appeared to be less specific than HPV testing of provider-collected specimens.

Clinical validation of the Cobas 4800 HPV assay using cervical samples in SurePath medium under the VALGENT4 framework

The VALidation of HPV Genotyping Tests (VALGENT) framework is an international cooperation designed for comparison and clinical validation of HPV assays with genotyping capabilities. Here we addressed the accuracy of the Roche cobas 4800 HPV test using SurePath samples from the Danish cervical cancer screening program under the VALGENT framework. The VALGENT4 panel comprises 998 consecutive SurePath cervical samples from routine screening and 297 SurePath samples enriched for disease (100 ASC-US, 100 LSIL, 97 HSIL). The cobas HPV test is a real-time PCR assay which detects HPV16 and 18 individually and 12 other high-risk (hr) HPV genotypes in one bulk. The clinical performance of the cobas test was assessed relative to that of the comparator assay GP5+/6 + PCR Enzyme ImmunoAssay (GP-EIA) by a non-inferiority test. The relative sensitivity for ≥ CIN2 was 1.00 (95% CI: 0.97-1.04) and relative specificity for the control group was 1.02 (95% CI: 1.01-1.04). The cobas test was found non-inferior to that of GP-EIA for both sensitivity and specificity (p-0.0006 and p < 0.0001, respectively). The type specific performance of the cobas test was evaluated using the GP5+/6 + PCR with Luminex genotyping (GP-LMNX) as comparator. The cobas test showed excellent to good concordance (Kappa: 0.70 to 0.90) with GP-LMNX for all three genotype groups in the overall VALGENT population but good to moderate concordance in the Screening population (kappa from 0.56 to 0.80). The cobas HPV test demonstrated non-inferiority to the comparator assay on cervical SurePath screening samples using the VALGENT4 panel.

Analytical and clinical performance of extended HPV genotyping with BD Onclarity HPV Assay in home-collected first-void urine: A diagnostic test accuracy study

Urine collection is a non-invasive self-sampling method offering the prospect of reaching women un(der)-screened for cervical cancer. The VALHUDES research framework was designed to address the lack of clinical accuracy data for high-risk (hr)HPV testing using urine samples. Here, we report on the analytical and clinical accuracy of hrHPV testing on first-void urine, collected at home, using an extended HPV genotyping assay. Paired first-void urine (Colli-Pee with UCM, Novosanis; index test) and clinician-collected cervical samples (Cervex-Brush, Rovers in PreservCyt Solution, Hologic; comparator test) were collected from 492 women aged 19 to 72 years attending colposcopy (reference test, with histology if indicated) (VALHUDES; NCT03064087). Extended HPV genotyping was performed on paired samples with the BD Onclarity HPV Assay. Cut-offs defined for cervical samples were also applied for first-void urine. HrHPV testing in first-void urine was similarly sensitive for both CIN2+ (ratio 1.00; 95% CI: 0.93-1.07) and CIN3 (ratio 0.98; 95% CI: 0.88-1.08), and marginally less specific for <CIN2 (ratio 0.92; 95% CI: 0.84-0.996) compared to cervical samples. HPV test agreement between sample pairs expressed as Cohen's Kappa (κ) was moderate to excellent for overall hrHPV and individual genotypes (or groups) (κ=0.56-0.85). BD Onclarity HPV Assay on first-void urine has similar clinical sensitivity and somewhat lower specificity to detect cervical precancer to testing on clinician-collected cervical samples.

Clinical performance of DNA and RNA based HPV tests for test of cure (TOC) post treatment for cervical intraepithelial neoplasia (CIN) - a retrospective study.

HPV testing as a "test of cure" (TOC) of women treated for cervical high-grade lesions can support and inform appropriate clinical management pathways. However, there is a lack of studies that report the discrete performance of different HPV assays in this context, including HPV mRNA based assays. To address this, we performed an analysis of the clinical performance of two hrHPV assays in the (TOC) setting; the recently launched DNA based Alinity m HR HPV (Abbott Molecular) and RNA based Aptima HPV assay (Hologic). Using a retrospective case-control design, two panels of archived cervical liquid based cytology samples, originally taken as per routine TOC protocols in Scotland were assessed. Each panel contained 63 cases, where cervical intraepithelial neoplasia 2 or worse (CIN2+) was detected and 160 controls (women with no CIN2+ and two subsequent cytology negative results (minimum) 3 years apart or women who had histologically confirmed ≤CIN1). All samples were previously tested using the RealTime High Risk HPV assay (Abbott Molecular) as per national TOC protocol. Panel A and Panel B were tested using Alinity and Aptima assay respectively. Both assays showed similar performance to the original RealTime assay. Aptima had sensitivity for CIN2+ of 96.8% (95% CI: 89.0- 99.6) compared to RealTime (93.7% (95% CI: 84.5 - 98.2)). Alinity had sensitivity for CIN2+ of 92.1% (95% CI: 82.4- 97.4) compared to RealTime (98.4% (95% CI: 91.5- 99.95)). Both mRNA based and DNA based HPV tests show robust performance for the monitoring of residual disease post-treatment.

Human papillomavirus negative high grade cervical lesions and cancers: Suggested guidance for HPV testing quality assurance

Some high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL). There were 116 initially HPV-negative cervical specimens (31 histopathology specimens and 85 liquid-based cytology samples) sent to the Swedish HPV Reference Laboratory for re-testing. Based on the results, an international QA guidance was developed through an iterative consensus process. Standard PCR testing detected HPV in 55.2 % (64/116) of initially "HPV-negative" samples. Whole genome sequencing of PCR-negative samples identified HPV in an additional 7 samples (overall 61.2 % HPV positivity). Reasons for failure to detect HPV in an HSIL+ lesion are listed and guidance to identify cases for extended re-testing, including which information should be included when referring samples to an NRL are presented. Monitoring the proportion of and reasons for failure to detect HPV in HSIL+ will help support high performance and quality improvement of HPV testing services. We encourage implementation of QA strategies based on re-analysis of "HPV negative" HSIL+ samples.

Performance of the Alinity m HR HPV assay on self-collected vaginal samples compared to clinician-collected cervical samples

Human papillomavirus (HPV) testing using self-collected samples could increase cervical cancer screening among never screened or underscreened populations. This study aimed to evaluate the concordance between self-collected and clinician-collected samples using the Alinity m high risk (HR) HPV extended genotyping assay. Self-collected vaginal samples and clinician-collected cervical samples were obtained from 25 to 69-year-old women who had visits for cervical cancer screening, colposcopy, follow up pap test, and/or treatment of cervical dysplasia at the George Washington University Hospital in Washington DC and Sarasota Memorial Health Care System and their affiliates in Florida. Extended genotyping based on the Alinity m HR HPV assay was performed on stored residual samples and the agreement between clinician- and self-collected HPV test results was assessed using positive percent agreement and Cohen's kappa values. There were 294 participants who provided paired self and clinician-collected samples. The overall prevalence of any HR-HPV was 26 %(76/293) for clinician-collected samples and 27 %(79/291) for self-collected samples. The positive percent agreement between clinician- and self-collected samples for any HR-HPV was 78 %, and the Cohen's Kappa value was 0.83(95 %CI:0.76,0.91). For specific HPV genotypes, the positive percent agreement ranged from 72 % for HPV16-79 % for other HR-HPV group A (HPV31/33/52/58); and the Kappa value ranged from 0.83(95 %CI:0.68,0.98) for HPV16-0.87(95 %CI:0.77,0.97) for other HR-HPV group A. There was a strong test concordance between self-collected and clinician-collected samples using the Alinity m HR HPV assay. Self-collected samples tested with the Alinity m HR HPV assays can be considered an alternative to clinician-collected primary HPV testing.

High-risk HPV mRNA testing on self-samples offered to those who do not attend for organised cervical screening – real world data from the Dumfries and Galloway region in Scotland

HPV self sampling can act as a tool to engage women in cervical screening and population based studies can inform optimal implementation of this approach. Self sampling kits were mailed to women who had defaulted from routine screening resident in an entire territorial health board in Scotland. Kit return rates and compliance to colposcopy follow up in those who were HPV mRNA positive were assessed. Concordance of the self-sample with samples taken later at colposcopy was measured alongside PPV of an mRNA positive result for CIN2+. Of 4173 women invited to participate, 20.5 %, returned their kit and a greater return rate with increasing age was observed. HPV mRNA positivity was 12.0 %, and invalidity rate was approximately 3 %. Compliance to colposcopy follow up was 88.3 % and the PPV for an mRNA test for CIN2+ on a self sample was 25.6 %. hr-HPV concordance on the initial swab and the follow up swab and liquid based cytology (LBC) sample taken at colposcopy was 67.1 % and 30 % respectively. HPV self sampling using a "mail to all" approach is feasible in Scotland although only 1 in 5 actively responded to the offer. Future work to monitor screening behaviours in those who were invited but did not engage initially will help quantify any additional benefit(s) incurred.

Validation of the clinical performance and reproducibility of the NeuMoDx HPV assay self-sample workflow

Human papillomavirus (HPV) testing on self-samples is a valid tool for cervical cancer screening. HPV self-sample workflows need to be clinically validated to ensure safe use in screening. This study evaluated the fully automated NeuMoDx HPV Assay self-sample workflow that is compiled of the NeuMoDx HPV assay and the NeuMoDx 96/288 Molecular Systems, for clinical performance and reproducibility on Evalyn Brush-collected self-samples. The clinical performance of the NeuMoDx HPV Assay self-sample workflow for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and CIN3+ was evaluated on 987 self-samples obtained from women attending national organized HPV-based cervical cancer screening by a noninferiority analysis relative to reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR. Intra- and inter-laboratory reproducibility of the NeuMoDx HPV Assay self-sample workflow using both NeuMoDx 96 and 288 Molecular Systems was assessed on 520 self-samples in three laboratories. The clinical sensitivity and specificity of the NeuMoDx HPV Assay self-sample workflow for the detection of CIN2+ and CIN3+ were found to be non-inferior to the reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR, with all p-values <0.034. The NeuMoDx HPV Assay self-sample workflow exhibited an intra-laboratory reproducibility of 94.4 % (95 %CI:92.5-96.1 %) with kappa value 0.86 (95 %CI:0.81-0.91). Inter-laboratory agreement was high (all ≥93.4 % and all kappa values ≥0.83). The NeuMoDx HPV Assay self-sample workflow demonstrated high clinical accuracy for CIN2+/3+ and high reproducibility. The NeuMoDx HPV Assay self-sample workflow can be considered suitable for cervical cancer screening purposes.

Allplex HPV HR Detection assay fulfils all clinical performance and reproducibility validation requirements for primary cervical cancer screening

Human papillomavirus (HPV)-based screening offers better protection against cervical cancer compared to cytology, but HPV screening assays must adhere to validation requirements of the international guidelines to ensure optimal performance. Allplex HPV HR Detection (Allplex) assay, launched in the late 2022, is a fully automated real-time PCR-based assay utilizing innovative technology that enables quantification and concurrent distinction of 14 high-risk HPV genotypes (HPV16,18,31,33,35,39,45,51,52,56,58,59,66 and 68). We assessed the validity of the Allplex for cervical cancer screening purposes, via comparison to a clinically validated comparator assay (Hybrid Capture 2; HC2), and through assessment of intra-laboratory reproducibility and inter-laboratory agreement. A clinical validation panel comprised of 973 residual ThinPrep samples was obtained from women aged 30-64 years participating in the organized Slovenian screening program, of these 863 were from women undergoing their regular screening visit after a previous negative screen test while 110 were from women with underlying cervical intraepithelial neoplasia grade 2 or worse (CIN2+) lesions. The Allplex's relative clinical sensitivity for detection of CIN2+ and CIN3+ were 1.01 (95%CI;0.98-1.04) and 0.98 (95%CI;0.95-1.02), compared to that of HC2. At recommended thresholds of ≥98% and ≥90%, the Allplex's clinical sensitivity and specificity (p=0.0004 and p=0.02, respectively) were non-inferior to HC2. High intra-laboratory reproducibility and inter-laboratory agreement, both overall (98.1% and 97.9%, respectively) and at genotype level (>98.7%) was observed. In addition, analytical genotype-specific performance of Allplex was compared to that of its predecessor Anyplex HPV HR; high overall agreement was observed (96.3%; kappa value 0.88), with some variations in performance. In conclusion, Allplex met all validation criteria described in the international guidelines on sensitivity, specificity and laboratory reproducibility and can be considered clinically validated for primary cervical cancer screening.

First international proficiency study on human papillomavirus testing in cervical cancer screening

Although cervical screening using Human Papillomavirus (HPV) testing is globally recommended public health policy, there has been no international proficiency studies specifically targeting HPV testing for cervical screening. To obtain the first global overview of the current proficiency of HPV testing services for cervical cancer screening. A coded proficiency panel of 12 samples containing HPV types 16, 18, 31, 33, 45, 52, 58 or 35/39/51/56/59/68 in human DNA in varying amounts as well as control. Datasets detecting at least a) 10 International Units (IU) of HPV16 and 18, b) 1000 IU of HPV types 31, 33, 45, 52, 58 and c) having no false positives were considered proficient. In total, 84 laboratories worldwide submitted 158 datasets (some laboratories used >1 HPV testing platform). Of those, 122 (77%) were 100% proficient. Only 14/158 datasets (9%) contained false positive results. Comparison of results with assays approved by the Food and Drug Administration (FDA) suggest that future proficiency requirements should also accommodate assays detecting only 100 IU of HPV16/18. A pool of low oncogenicity HPV types that contributed very little to sensitivity, but adversely affected specificity, was detectable by most datasets. Internationally recognized proficiency studies of HPV screening, traceable to international standards, provided an overview of current testing performance. There was a high level of proficiency in terms of sensitivity and few false positives, but specificity was not optimal and further research on optimal specificity of HPV screening tests may be warranted.

The Allplex HPV HR Detection assay fulfils international guideline requirements for primary cervical screening on SurePath samples and qualifies as a second-generation HPV comparator test

A key parameter for the continued success of cervical cancer screening is quality-controlled use of human papillomavirus (HPV) tests that are clinically validated according to international guidelines. The clinical accuracy for cervical screening of the Allplex HPV HR Detection (Allplex), which concurrently detects and distinguishes 12 high-risk HPV types (16,18,31,33,35,39,45,51,52,56,58,59) and HPV66 and HPV68 was assessed on SurePath samples by comparing its performance to the second-generation comparator BD Onclarity HPV assay (Onclarity). The absolute clinical sensitivity, assessed on 76 samples derived from a screening population with underlying CIN2+, of Allplex and Onclarity was 98.7 % (95 % CI, 92.9-100.0 %) and 100.0 % (95 % CI, 95.2-100.0 %), respectively, with relative sensitivity of Allplex of 0.99 (95 % CI; 0.96-1.01). The absolute clinical specificity, assessed on 801 consecutive clinician-collected cervical samples obtained from women 30 to 59 years old attending the routine Danish cervical screening program, for Allplex and Onclarity was 92.5 % (95 % CI, 90.4-94.2 %) and 92.5 % (95 % CI, 90.4-94.2 %), respectively, with relative specificity of Allplex of 1.00 (95 % CI; 0.99-1.01). With thresholds mandated by international guidelines of ≥90 % for relative clinical sensitivity (p = 0.001) and ≥98 % for relative clinical specificity (p = 0.0018), Allplex was non-inferior to Onclarity. Excellent intra- and inter-laboratory agreement of Allplex was observed, both overall (99.2 % and 99.6 %) and at the genotype level (range: 99.6-100.0 %). By fulfilling all guideline requirements for clinical sensitivity, specificity, and reproducibility, Allplex can be considered clinically validated for primary cervical screening using clinician-collected SurePath samples. With this study, Allplex also meets the criteria for a second-generation HPV comparator test.

The 2019 HPV Labnet international proficiency study: Need of global Human Papillomavirus Proficiency Testing

Accurate and internationally comparable human papillomavirus (HPV) testing services are essential for cervical cancer elimination programs. The WHO HPV Laboratory Network started issuing international HPV testing proficiency panels in 2008. We report the results of the 2019 global proficiency study and evaluate the proficiency over time. The proficiency panel contained 40 coded samples containing mixes of purified HPV types (HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/68a/68b) and 4 controls. Proficiency required detection of both single and multiple infections of 50 International Units of HPV 16/18, of 500 genome equivalents (10x higher concentration) for other HPV types, and no false positives (stricter requirement compared to previous panels). Seventy-eight laboratories submitted 110 datasets with 38 different assays. Most samples (38/44) were reported with 100% proficiency in most datasets. Mostly commercial assays were used (88/110 datasets). Overall, 47.3% of the datasets were 100% proficient. False positivity was detected in at least one sample in 30.1% of datasets. When analysing all datasets ever since 2008 using exactly the same proficiency criteria, there was a steady improvement up to 2017 (the proportion of datasets being completely proficient increased from 25% to 73%). However, in the 2019 proficiency testing the proportion of fully proficient datasets dropped to 50%. Although we initially documented a worldwide improvement in comparability and reliability of HPV testing services, the trend now appears to be reversed. In response, the International HPV Reference Center will provide support for improved quality of laboratory services, including issuing of global proficiency panels every year.

Improving human papillomavirus (HPV) testing in the cervical cancer elimination era: The 2021 HPV LabNet international proficiency study

Proficient Human Papillomavirus (HPV) genotyping services are essential to support HPV and cervical cancer elimination strategies, in particular to support HPV vaccine research. To perform a global HPV genotyping proficiency study, with evaluation in relation to previous proficiency studies. The proficiency panel contained 44 coded samples (40 samples containing one or more purified HPV types (HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/68a/68b) in human DNA, 1 human DNA control and 3 DNA extraction controls). Proficiency required detection of both single and multiple infections of 50 International Units of HPV 16/18, of 500 genome equivalents for other HPV types and no false positivity. One hundred and thirty-two laboratories submitted 211 datasets. Most assays used (182/211 datasets) were commercially available. An all-time high of 75% of the datasets were 100% proficient. One or more false positives were found in 17.5% of datasets. Among laboratories who participated in the 2019 proficiency study, full proficiency increased from 25% in 2019 to 60% in 2021. The high overall proficiency was mostly attributable to a large number of new laboratories, which used similar assays. The worldwide deterioration in comparability and reliability of HPV testing found in 2019 is now reversed and an overall increase in proficiency is found.

The challenges of defining sample adequacy in an era of HPV based cervical screening

The implementation of Human Papillomavirus based cervical screening continues apace on a global scale. Understanding the basis and burden of inadequate or invalid samples is important to ensure confidence in high quality laboratory results and inform the development of new technologies. Here we present population based data from Scotland and Denmark which detail the extent of invalid samples for HPV detection in both clinician-taken and self-taken samples. As a comparator we report on the rate of inadequate cytology preparations in both countries. The proportion of samples with an invalid HPV test result was calculated by retrospective analysis of routine laboratory data associated with cervical screening programmes in the two countries. Two assays were in use for the programmes at the time (the Abbott RealTime High Risk HPV assay and the BD Onclarity); both have internal endogenous controls for human genes. In addition, acellular cytology samples were reported through a prospective audit (Scotland) and National quality reporting (Denmark). In total, 89,418 clinician samples and 14,677 self-taken samples were assessed. We observed low rates of invalid HPV tests in clinician taken samples (0.05-0.10 %), irrespective of sample collection media (ThinPrep or SurePath), HPV test system/endogenous control type or clinical indication for testing (primary screening, triage or test of cure). For self-taken samples, the number of invalid samples was 0.18 %. Complete absence of sample material (acellular) in clinician taken samples were observed at a level of 1 in approximately 16.5 thousand. Clinician and self-taken samples appear robust specimens for HPV testing and acellular samples are very rare. Efforts to develop endogenous controls for HPV assays that provide greater insight into true sample adequacy for cervical disease detection, beyond measuring the presence of human cells, will be welcome.

Comparison of the clinical and analytical performance of Alinity m HR HPV and cobas 4800 HPV assays in a population-based screening setting

The recently launched Abbott Alinity m HR HPV (Alinity) assay separately identifies high-risk human papillomavirus (hrHPV) genotypes HPV16, HPV18, and HPV45, and reports 11 other genotypes as two aggregates. Clinical and analytical performance of Alinity was compared with the cobas 4800 HPV assay on 4,334 women aged 20-64 years attending routine, population-based organized cervical cancer screening during 2009/2010. After 36 months, they were invited to participate in the second screening round (2012-2014) and later followed-up through centralized national cervical cancer screening registry. In women 30 and older, the clinical sensitivity for cervical intraepithelial neoplasia grade 2+ (CIN2+) was 100.0% (95% CI, 88.2-100.0%) for Alinity and 100.0% (95% CI, 88.2-100.0%) for cobas, and for CIN3+ 100.0% (95% CI, 78.9-100.0%) for both assays. The clinical specificity for ≤ CIN1 in women 30 and older was 92.4% (95% CI, 91.4-93.3%) and 92.9% (95% CI, 91.9-93.7%), respectively. The assays demonstrated excellent overall agreement for hrHPV detection (97.9%) and genotype-specific agreement for HPV16 (99.6%), HPV18 (99.8%), and other hrHPV (98.1%). Overall positive agreement and positive agreements for HPV16, HPV18, and other hrHPV genotypes were 84.3%, 89.1%, 73.2%, and 82.3%. Based on a 5-year CIN3+ risk, slightly more HPV-positive women would require referral to immediate colposcopy after testing with Alinity vs. cobas (4.1% vs. 3.8%; p = 0.470), but significantly fewer Alinity-tested women would need a 6- to 12-month follow-up visit compared with those tested with cobas (5.0% vs. 8.6%; p < 0.0001). Alinity and cobas have comparable clinical performance and showed excellent overall and genotype-specific agreement. The Alinity's extended genotyping ability could help predict the 5-year CIN3+ risk and cost-saving management of HPV-screen-positive women.

Development of a large biorepository of cervical specimens for the Improving Risk Informed HPV Screening study (IRIS)

Biomarkers of Human Papillomavirus (HPV) cervical carcinogenesis are critical to address questions of how to triage and manage women who screen positive for high-risk HPV (HrHPV) and identify those at highest cancer risk. We describe the development of a large biorepository of cervical specimens for the Improving Risk Informed HPV Screening Study (IRIS) using residual specimens collected in the regional laboratory from women aged 25 and older who had cervical cancer screening or follow-up testing with high-risk human papillomavirus (HrHPV) testing and liquid-based cytology (co-testing) at Kaiser Permanente Northern California (KPNC) from January 2016 to August 2018. Specimen selection, processing for long-term storage, follow-up tracking, consent and demographic and clinical characteristics of the women in the IRIS cohort are described. Selecting from 897,680 women who had at least one co-test during the study period, we collected 199,403 baseline and 216,390 follow-up HrHPV and cytology specimens from a stratified random sample of 81,348 women, of which 3,428 (4.2%) opted out of the study and were excluded. The majority (79.9%) of the baseline specimens were from HrHPV-positive women. The mean age was 36 years, and the cohort is racially/ethnically diverse with 56% of women being Hispanic or non-white. Over two-thirds of the cohort were members of KPNC for two or more years prior to inclusion. Of the 77,920 women included in the cohort, 57,414 (73.7%) had at least one follow-up co-test. Use of specimens from the biorepository will elucidate molecular mechanisms underlying HPV carcinogenesis and inform more effective screening and follow-up strategies.

Comparative analysis between self-collected and clinician-collected samples for HPV testing in public health facilities in Zimbabwe

Cervical cancer screening programs that use visual inspection with acetic acid to identify women with pre-cancerous lesions in Zimbabwe have had limited success due to challenges with human resource constraints and patient acceptability. Nucleic acid amplification tests for human papillomavirus (HPV) have been endorsed by the World Health Organization for cervical cancer screening, along with self-collection of samples. As evidence shows self-collected sampling to be acceptable and preferable, Zimbabwe's Ministry of Health and Child Care (MOHCC) required a comparative analysis on the agreement between self- and clinician-collected samples for testing with Hologic Aptima HPV mRNA assay, to determine if self-collected samples could be used as another method to increase coverage of cervical cancer screening programs. In four public health facilities in Zimbabwe from July to August 2020, self- and clinician-collected HPV samples were obtained from HIV-positive women aged 30-49 years for HPV testing. A total of 280 self- and clinician-collected samples were tested and results were found to have good agreement (κ: 0.75, 95% CI: 0.66-0.82). HPV prevalence was 43.0% (95% CI: 37.0%-49.3%) for self-samples and 48.0% (95% CI: 41.0%-54.2%) for clinician-samples. Self-collected sampling had good agreement with clinician-collected and its inclusion in the national cervical cancer screening policy by Zimbabwe's MOHCC is expected to increase testing coverage, especially among underserved communities such as women living with HIV, as well as decentralize access to cervical cancer screening services for lower-level facilities and increase the geographical scope of where HPV testing can be offered through the country.