Laila Sara Arroyo Mühr

E6/E7 Similarity to Human Papillomavirus Prototypes and Performance of HPV Testing by Cobas 4800 HPV Test and Anyplex II HPV HR

ABSTRACT Human papillomavirus (HPV) genotype classification relies on DNA sequence similarity to reference (prototype) sequences. Most HPV assays used for cervical cancer screening were clinically validated against European HPV prototypes. However, the impact of HPV sequence polymorphisms on test performance remains unexplored. We evaluated whether sequence variation in E6/E7 relative to HPV prototypes affects test performance by analyzing cervicovaginal samples from 990 women enrolled (2019‐2022) across Belgium, Portugal, Brazil and Ecuador. Samples were tested using cobas, Anyplex, and next‐generation sequencing (Ampliseq/Ion Torrent targeting E6/E7). Sequence variation was defined as the proportion of single nucleotide polymorphisms across E6/E7 relative to reference sequence. Sequence variation was, on average, higher in HPV‐negative than HPV‐positive samples for HPV16 (0.46% vs 0.13%) and HPV18 (0.44% vs 0.37%) using cobas. Similar patterns were observed with Anyplex (HPV16: 0.78% vs 0.13%, HPV33: 0.66% vs 0.40%, HPV58: 0.79% vs 0.53, and HPV66: 1.14% vs 0.25%). For HPV45, sequence variation was, on average, higher in HPV‐positive than HPV‐negative samples when tested with Anyplex (0.87% vs 0.43%). For HPV types 18, 31, 35, 39, 51, 52, 56, 59 and 68, the mean sequence variation was similar between HPV‐negative and HPV‐positive samples using Anyplex. Our findings show that sequence variation relative to prototypes may impact test performance.

Nationwide implementation and evaluation of an external quality assessment program for HPV screening in Peru

In the global effort to eliminate cervical cancer, high-quality Human Papillomavirus (HPV) testing is essential, especially in Peru where vaccination coverage remains incomplete. To ensure consistent nationwide test performance, the Peruvian HPV National Reference Laboratory (NRL), in collaboration with the International HPV Reference Center (IHRC), launched the first nationwide External Quality Assessment (EQA) program for all screening laboratories. In 2024, 19 screening laboratories, including regional reference centers and tertiary hospitals, participated in the EQA program. Proficiency panels of 13 blinded samples with defined HPV types and viral loads were validated by IHRC and distributed by the NRL. Laboratories analyzed the samples using the Cobas 4800 HPV assay. Eighteen laboratories (94.7%) met proficiency criteria, correctly detecting all required HPV types, including low viral load samples. One laboratory reported false positives in a negative and a low-concentration HPV 18 sample. This program shows the feasibility of nationwide EQA in Peru, with full participation and reporting. Annual assessments will sustain quality assurance and equitable access to reliable HPV testing. From 2026, the Peruvian HPV NRL will coordinate the program independently, expand participation to additional laboratories, and enable local panel production-an important step toward strengthening cervical cancer screening quality.

Viability of Self‐Taken Vaginal Swab Samples for RNA‐Based Biomarker Analysis in Cervical Disease

ABSTRACT High risk human papillomaviruses (hrHPVs) cause most cervical cancers. Cervical screening programmes aim to identify precancerous disease using detection of hrHPV nucleic acid using clinician‐taken liquid‐based cytology (LBC) samples, or increasingly, self‐taken samples (STSs). However, STSs are incompatible with traditional cytology triage. Therefore, development of novel triage tests is essential. Quantification of cellular and viral mRNA biomarkers is one option, but little is known about mRNA quality in STSs. We extracted RNA from two sets of STSs (reflecting separate sampling devices) from the Scottish HPV Archive (SHA) and the Swedish Cervical Cytology Biobank (SCCB). We investigated whether the ACTB , GAPDH and p16 RNAs could be amplified by reverse transcription quantitative PCR (RT‐qPCR). RNA was degraded in both sets of samples, but samples from the Scottish HPV Archive were generally suitable for RT‐qPCR analysis, while samples from the SCCB were mostly unsuitable. Genomic DNA contamination was detected in 11.6% of samples. The quantity and quality of RNA derived from STSs was unaffected by storage of the original sample at −70°C for a period of 1 year. These data suggest that feasibility of utilising STSs for mRNA expression work is device‐dependent and that optimisation of collection and storage systems is warranted.

Nationwide registry‐based trial of risk‐stratified cervical screening

AbstractIn well‐screened populations, most cervical cancers arise from small groups of women with inadequate screening. The present study aims to assess whether registry‐based cancer risk assessment could be used to increase screening intensity among high‐risk women. The National Cervical Screening Registry identified the 28,689 women residents in Sweden who had either no previous cervical screening or a screening history indicating high risk. We invited these women by SMS and/or physical letter to order a free human papillomavirus (HPV) self‐sampling kit. The Swedish national HPV reference laboratory performed extended HPV genotyping and referred high‐risk HPV‐positive women to their regional gynecologist. A total of 3691/28,689 (12.9%) women ordered a self‐sampling kit and 10.0% (2853/28,689) returned a sample for testing. Participation among women who had never attended screening was low, albeit improved. Up to 22.5% of women in other high‐risk groups attended. High‐risk HPV types were detected in 8.3% of samples. High‐risk HPV‐positive women (238/2853) were referred without further triaging and severe cervical precancer or cancer (HSIL+) in histopathology were detected in 36/158 (23%) of biopsied women. Repeat invitations gave modest additional participation. Nationwide contacting of women with high risk for cervical cancer with personal invitations to order HPV self‐sampling kits resulted in high yield of detected CIN2+. Further efforts to improve risk‐stratified screening strategies should be directed to improving (i) the precision of the risk‐stratification algorithm, (ii) the convenience for the women to participate and, (iii) ensuring that screen‐positive women are followed‐up.

The Swedish Cervical Screening Cohort

AbstractThe Cervical Screening Cohort enrols women screened for human papillomavirus (HPV) and cervical abnormalities within the capital region of Sweden from the organised screening program and the non-organised testing of cervical samples. The cohort started in 2011 and has enrolled more than 670,000 women, contributing with more than 1.2 million biobanked samples. The cohort is systematically updated with individual-level data from the Swedish National Cervical Screening Registry (NKCx). Key variables include birthdate, sampling date, cytological, histopathological and HPV analysis results, and invitation history. Each sampling and subsequent clinical follow-up is sequentially registered, allowing for longitudinal analyses of screening results and associated results of the clinical workup. The cohort is ideal for longitudinal, long-term follow-up studies due to its validated documentation and registry-derived information. From the data, it is possible to penetrate important human health mechanisms. The data are available as open-data and GDPR-compliant. Samples are available after getting the required permissions. Results will help researchers understand factors that increase cancer risk and other diseases.

Concomitant human papillomavirus (HPV) vaccination and screening for elimination of HPV and cervical cancer

Abstract HPV vaccination with concomitant HPV-based screening of young women has been proposed for faster cervical cancer elimination. We describe the baseline results of a population-based trial of this strategy to reduce the incidence of HPV. All 89,547 women born 1994-1999 and resident in the capital region of Sweden were personally invited to concomitant HPV vaccination and HPV screening with 26,125 women (29.2%) enrolled between 2021-05-03 and 2022-12-31. Baseline HPV genotyping of cervical samples from the study participants finds, compared to pre-vaccination prevalences, a strong decline of HPV16 and 18 in birth cohorts previously offered vaccination, some decline for cross-protected HPV types but no decline for HPV types not targeted by vaccines. Our dynamic transmission modelling predicts that the trial could reduce the incidence of high-risk HPV infections among the 1994-1998 cohorts by 62-64% in 3 years. Baseline results are prevalences of HPV infection, validated transmission model projections, and power estimates for evaluating HPV incidence reductions at follow-up (+/−0.1% with 99.9% confidence). In conclusion, concomitant HPV vaccination and HPV screening appears to be a realistic option for faster cervical cancer elimination. Clinicaltrials.gov identifier: NCT04910802; EudraCT number: 2020-001169-34.

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.

Audit of laboratory sensitivity of human papillomavirus and cytology testing in a cervical screening program

AbstractThe globally recommended public health policy for cervical screening is primary human papillomavirus (HPV) screening with cytology triaging of positives. To ensure optimal quality of laboratory services we have conducted regular audits of cervical smears taken before cervical cancer or cancer in situ (CIN3+) within an HPV‐based screening program. The central cervical screening laboratory of Stockholm, Sweden, identified cases of CIN3+ who had had a previous cervical screening test up to 3 years before and randomly selected 300 cervical liquid‐based cytology (LBC) samples for auditing. HPV testing with Roche Cobas was performed either at screening or with biobanked samples. HPV negative samples and subsequent biopsies were retrieved and tested with modified general primer HPV PCR and, if still HPV‐negative, the LBCs and biopsies were whole genome sequenced. The Cobas 4800 detected HPV in 1020/1052 (97.0%) LBC samples taken before CIN3+. Further analyses found HPV in 28 samples, with nine of those containing HPV types not targeted by the Cobas 4800 test. There were 4 specimens (4/1052, 0.4%) where no HPV was detected. By comparison, the proportion of CIN3+ cases that were positive in a previous cytology were 91.6%. We find that the routine HPV screening test had a sensitivity in the real‐life screening program of 97.0%. Regular laboratory audits of cervical samples taken before CIN3+ can be readily performed within a real‐life screening program and provide assurance that the laboratory of the real‐life program has the expected performance.

Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR

Abstract Background Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples. Methods Using Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers. Results HPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1–93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392). Conclusions Unbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.

Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers

Human Papillomavirus Infection Determines Prognosis in Cervical Cancer

PURPOSE Detection of human papillomavirus (HPV) by polymerase chain reaction in invasive cervical cancer is strongly associated with prognosis but previous studies have not considered sequencing efforts. We aimed to assess the association when also including comprehensive analysis of HPV infection by deep sequencing and a longer follow-up period. MATERIALS AND METHODS We subjected all 392 of 2,845 invasive cervical cancer cases that were polymerase chain reaction–negative for HPV to RNA sequencing on the NovaSeq 6000 platform (Illumina) and identified an additional 169 cases as HPV-positive. We followed all women from date of diagnosis to December 31, 2016, emigration, or death, whichever occurred first. The main outcome was all-cause mortality by December 31, 2016. We calculated 5-year cumulative relative survival ratios compared with the female general population and used Poisson regression to estimate excess hazard ratios of all-cause mortality by infection with any of the 13 most oncogenic (high-risk [hr]) HPV types in the tumor. All models were adjusted for age, time since diagnosis, stage, histology, and education level. RESULTS The 5-year cumulative relative survival ratio was 0.45 (95% CI, 0.39 to 0.51) in the hrHPV-negative group, and 0.74 (95% CI, 0.72 to 0.75) in the hrHPV-positive group. This translated to a statistically significantly 43% lower excess mortality in the hrHPV-positive group compared with the hrHPV-negative (corresponding to an excess hazard ratio 0.57; 95% CI, 0.48 to 0.69). There was no association between HPV risk group, clade, or number of HPV infections and prognosis. CONCLUSION hrHPV status is a strong determinant of cervical cancer prognosis over 15 years after diagnosis, above and beyond other established factors.

The International Human Papillomavirus Reference Center: Standardization, collaboration, and quality assurance in HPV research and diagnostics

AbstractThe International Human Papillomavirus (HPV) Reference Center (IHRC) confirms and assigns type numbers to novel HPV types, maintains a reference clone repository, and issues international proficiency panels for HPV screening and genotyping. Furthermore, the Center coordinates the Global HPV Reference Laboratory Network that promotes collaboration and international exchange of experiences among national HPV reference laboratories, to further international standardization and quality assurance in the HPV field. The established HPV types (n = 225) belong to 5 different genera: alpha (n = 65), beta (n = 54), gamma (n = 102), mu (n = 3) and nu (n = 1). Since the last published IHRC overview in 2018, 6 novel types have been established, with 5/6 belonging to the gamma genus and 1/6 to beta genus. Also, 474 reference clones have been provided to 55 different research laboratories and the global proficiency program for HPV genotyping has seen an increasing proficiency (despite a decrease seen in 2019), from 68% proficiency in 2017 to 77.3% in 2022. The first proficiency study for HPV screening found an international proficiency of up to 77%. In summary, increasing complexity of the HPVs and demands on quality assurance in the era of cervical cancer elimination requires international efforts to support proficiency and recognized quality and order among HPV types.

Quality Assurance in Cervical Cancer Screening: Evaluation of Sample Adequacy in HPV DNA Testing

ABSTRACTIn HPV‐primary screening, sample quality significantly influences test accuracy. Unlike cytology‐based screening, no consensus guidelines presently exist for sample quality assessment in HPV testing. This study aims to evaluate the impact of sample cellularity on HPV testing. A total of 37 592 liquid‐based cytology (LBC) samples from women undergoing HPV‐primary screening (aged 30–64, median 48; IQR: 40–56 years) were analyzed using Cobas 4800 HPV Test (Roche). Sample adequacy was assessed by the assay's β‐globin internal control and by an independent quantitative cellularity assessment (OncoPredict HPV, Hiantis). HPV positivity rates (PR) were stratified according to β‐globin Ct values. Among the analyzed samples, 50.0%, 47.1%, 2.3%, and 0.6% had β‐globin Ct values of ≤ 28, > 28 to ≤ 32, > 32 to ≤ 34, and > 34, respectively. Overall HPV‐PR was 7.7% (2891/37 592). PR reached 9.7% in samples with β‐globin ≤ 28 Ct (1820/18 801), decreasing markedly to 1.4% for β‐globin > 34 Ct (3/214), (p < 0.001). Quantitative analysis showed that Cobas 4800 β‐globin Ct = 34 corresponds to approximately 1.5 × 10^3 nucleated cells/reaction. A subset of 195 HPV‐negative samples with β‐globin Ct ≥ 34 was evaluated by liquid based cytology (LBC): 19% had inadequate cellularity according to LBC guidelines, 8% were ≥ ASC‐US and 73% NILMs. 65% of adequate LBC showed cellular atrophy. These findings emphasize the importance of assessing cellularity in HPV‐screening to avoid potentially false‐negative results due to inadequate samples. Future research should focus on establishing standardized cellularity thresholds to improve screening accuracy.

Concomitant HPV Vaccination and HPV Screening HPV Infection and Cervical Cancer in Sweden

The study aims to evaluate whether organised, concomitant HPV vaccination and HPV screening offered to all resident women aged 22-27 will result in a more rapid elimination of HPV infection in Sweden. This objective will be examined at the population level.

Research Project on Reminders and Self-Sampling Can Increase Participation in Gynecology Cell Sampling - Preventive Examination Against Cervical Cancer.

Prevention of cervical cancer with cervical screening is one of the most successful screening activities in medicine. In Sweden, screening was implemented in the 1960s and has since prevented tens of thousands of women from having cervical cancer. Individual invitations to screening result in increased attendance therefore evaluating strategies for reaching women through invitations is particularly valuable. Women who regularly attend screening following an invitation reduce their risk of cervical cancer by as much as 90%. Of the women who are diagnosed with cervical cancer (about 550 women per year in Sweden), as many as 38% did not participate in the screening. Invitations for screening are sent to the entire population in Sweden aged 23-70. The current coverage of screening is 82.9%, which represents the proportion of women ages 23-70 who attend according to recommendations. In addition, many women are sporadic attenders who reduce their risk for cancer somewhat. The highest cancer risk is seen among those women who have never participated as well as women who have had a history of precancerous lesions or HPV infection but have not been followed-up. Cervical cancer is the first form of cancer for which there are approved molecular screening tests (HPV test). Unlike the older screening method (cytology), self-collected samples can be analyzed for HPV (the analysis method is so sensitive that it does not matter if the sample is not optimally taken). Invitations and reminders about cervical screening are sent by letter to the woman's home address (about 3 million letters per year in Sweden). This strategy results in a waste of resources and has a negative environmental impact. Regarding reminders, we have seen in previous research that the effect is not optimal. When sending a physical reminder letter to women who have not participated in more than 10 years (current routine), only 2% of the women invited came for sampling. Reminders with SMS are now standard for many businesses in society, such as car testing or dental appointments. It is inexpensive, saves the environment and there are studies that suggest it is more effective than sending physical letters. In this study, we intend to investigate whether SMS reminders, electronic letters, and physical letters for screening lead to increased participation and thus to a higher proportion of detected, treatable precursors of cervical cancer compared to before.