Assessment of a new low-cost, PCR-based strategy for high-risk human papillomavirus DNA detection for cervical cancer prevention

Detection and Genotyping of Papillomavirus by Real-Time PCR in Iraqi Patients

Background: Cervical cancer (CC) is linked to human papillomavirus (HPV). Globally, the prevalence and genotype distribution differ significantly. Objectives: The goal of this study was to find HPV 14, 16, 18, and 45 genotypes in urogenital swabs by using a real-time PCR amplification test for quantitative genotyping of HPV DNA types 16, 18, and 45 and for simultaneous quantitative detection of HPV DNA types 31, 33, 35, 39, 51, 52, 56, 58, 59, 66, and 68, for a total of 14 HPV genotypes. Methods: This case-control study included 86 cervical swabs from Iraqi women referred by the Al-Yarmook teaching hospital in Baghdad, Iraq. The ages of cases varied from 23 to 70 years and specimens were obtained between March 2020 and March 2021. The DNA was extracted for molecular assay. Fourteen HPV genotypes were detected using real-time PCR (16, 18, 45, 31, 33, 35, 39, 51, 52, 56, 58, 59, 66, and 68). The detection protocol was based on the commercial Kit V31-100/F FRT as follows. For each sample reaction, 10х(N+1) μL of PCR-mix-1-FRT HPV 14 was added into a new tube. Then, 5.0х(N+1) μL of PCR-mix-2 buffer and 0.5х(N+1) μL of TaqF DNA polymerase were added. The tubes were vortexed. Finally, the prepared tubes added 10 μL of DNA samples from test or control samples. The statistical analysis was conducted using the statistical package for SPSS and Excel 2016 software. Results: Genotype 16 had the highest frequency, followed by genotypes 45 (22%), 18 (14%), 35 and 59 (6%), 52 and 58 (4%), and 31 (2%), while genotypes 33, 39, 51, 56, 66, and 68 had the lowest frequency (1%). Conclusions: The real-time PCR was efficient for detecting and genotyping HPV-DNA and could help in earlier detection and clinical care of HPV-infected patients by reducing costs and workload.

Assessing Barriers Encountered by Women in Cervical Cancer Screening and Follow-Up Care in Urban Bolivia, Cochabamba

Background: Timely detection of cervical cells infected with high-risk human papillomavirus (HPV) improves cervical cancer prevention. In Bolivia, actual screening coverage only reaches 33.3% of the target population aged between 25 and 64 years despite free cytology screening. Furthermore, 50% to 80% screened women are lost during follow-up. This study aimed at identifying factors explaining this lack of follow-up care. Method: During the first phase, face-to-face semi-structured interviews were conducted with HPV-positive women. Secondly, we explored the reasons for the non-adherence to the follow-up care: knowledge, perceptions and beliefs about HPV, as well as barriers to healthcare access, using a structured survey on Cochabamba women and healthcare professionals. Results: Barriers to effective follow-up of the targeted populations were associated with health system shortcomings, including poor service delivery at the front- and second-line, health providers shortage, inadequate training, waiting time, high direct and indirect costs of care seeking and care, complex procedures to obtain HPV screening results and poor patient–provider communication. The follow-up was perceived as extremely stressful by the participants. Conclusion: Improved communication on HPV and HPV-related cancers in terms of representation in the general population and among the health professional’s population is vital to improve access for HPV infection follow-up care.

End-to-end computational approach to the design of RNA biosensors for detecting miRNA biomarkers of cervical cancer

Cervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Relatively scant awareness and limited access to effective diagnosis have led to this enormous disease burden, calling for point-of-care, minimally invasive diagnosis methods. Here, an end-to-end quantitative unified pipeline for diagnosis has been developed, beginning with identification of optimal biomarkers, concurrent design of toehold switch sensors, and finally simulation of the designed diagnostic circuits to assess performance. Using miRNA expression data in the public domain, we identified miR-21–5p and miR-20a-5p as blood-based miRNA biomarkers specific to early-stage cervical cancer employing a multi-tier algorithmic screening. Synthetic riboregulators called toehold switches specific to the biomarker panel were then designed. To predict the dynamic range of toehold switches for use in genetic circuits as biosensors, we used a generic grammar of these switches, and built a neural network model of dynamic range using thermodynamic features derived from mRNA secondary structure and interaction. Second-generation toehold switches were used to overcome the design challenges associated with miRNA biomarkers. The resultant model yielded an adj. R² ∼0.71, outperforming earlier models of toehold-switch dynamic range. Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers. Simulations showed a linear response between 10 nM and 100 nM before saturation. Our study demonstrates an end-to-end computational workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic/nucleic-acid signatures. The approach has the potential to replace iterative experimental trial and error, and focus time, money, and efforts. All software including the toehold grammar parser, neural network model and reaction kinetics simulation are available as open-source software (https://github.com/SASTRA-iGEM2019) under GNU GPLv3 licence.

Digital Hybridization Human Papillomavirus Assay with Attomolar Sensitivity without Amplification

Detection of nucleic acid without amplification can avoid problems associated with thermal cycling such as labor-intensiveness and aerosol pollution. Here we develop a droplet-based digital microfluidic hybridization assay for nucleic acid detection with attomolar sensitivity. This assay provides a clinically useful sensitivity for detecting human papillomavirus (HPV) without amplification. The sensitivity is accomplished using femtoliter-sized droplet microfluidics for concentrating enzyme-catalyzed fluorescent products into a detectable signal and magnetic beads for accelerating reaction time. Meanwhile, using magnetic beads and droplet microfluidic chips, we can improve the sampling efficiency over conventional methods. We characterized the sensitivity, selectivity, detection range, stability, and accuracy of our assay. Our assay is 50-fold more sensitive than the traditional hybrid capture assay. The assay without amplification avoids problems of complex handling procedures and aerosol pollution. The direct and sensitive detection of nucleic acid using a droplet microfluidic system provides an early disease diagnosis tool.

Comparative analysis of different PCR-based strategies for HPV detection and genotyping from cervical samples

BACKGROUND

Human papillomavirus (HPV) is the main cause of cervical cancer. Polymerase chain reaction (PCR)-based techniques are associated with accurate results with respect to HPV detection and genotyping, being able to identify viral DNA at low levels. However, differences in primer design influence their sensibility and specificity, depending on the HPV type assessed.

OBJECTIVE

The aim of the study was to comparatively evaluate the effectiveness of three different PCR-based strategies for HPV detection and genotyping from cervical samples.

STUDY DESIGN

The procedures were based on different primer design strategies, using MY09/MY11, EntroA, and type specific multiplex PCR primers.

RESULTS

Out of 411 samples of cervical scrapings, 45 (10.9%), 50 (12.2%), and 117 (28.5%) were positive for MY09/MY11, EntroA, and multiplex PCR, respectively. For MY09/MY11 positive samples, 36 were negative for EntroA and 23 for multiplex PCR. For EntroA positive samples, 40 were negative for MY09/MY11 and 26 for multiplex PCR. For multiplex PCR positive samples, 96 were negative for MY09/MY11 and 94 for EntroA. MY09/MY11 identified 12 different HPV types, EntroA detected eight types and multiplex PCR detected 11 HPV types. EntroA primers were able to detect HPV in more samples than MY09/MY11, while multiplex PCR, despite the limited targeted HPV types, presented higher sensibility than the other methods.

CONCLUSIONS

The three methods presented different advantages and disadvantages, and the present study reinforces the need to use more than one molecular strategy for HPV detection and genotyping, and the development of novel methods which could overcome the limitations of the existing tests.

Agreement between careHPV and hybrid capture 2 in detecting high-risk HPV in women in Tanzania

INTRODUCTION

Visual inspection of the cervix with acetic acid is used to control the burden of cervical cancer in low- and middle-income countries. This method has some limitations and HPV DNA testing may be an alternative, but it is expensive and requires a laboratory setup. Cheaper and faster HPV tests have been developed. This study describe the agreement between a fast HPV test (careHPV) and hybrid capture 2 (HC2) in detection of high-risk HPV among Tanzanian women.

MATERIAL AND METHODS

The study involved women attending routine cervical cancer screening at the Ocean Road Cancer Institute and Kilimanjaro Christian Medical Centre in Tanzania. The women were offered HIV testing. Two cervical samples were subsequently obtained; the first sample was processed at the clinics using careHPV and the second sample was transported to Denmark and Germany for cytology and HC2 analysis. Kappa statistic was calculated to assess the agreement between careHPV and HC2. The sensitivity, specificity and predictive values of careHPV were calculated using HC2 as reference. The analyses were done for the overall study population and stratified by testing site and HIV status.

RESULTS

A total of 4080 women were enrolled, with 437 being excluded due to invalid information, lack of careHPV or HC2 results. Overall agreement between the tests was substantial with a kappa value of 0.69 (95% confidence interval [CI] 0.66-0.72). The sensitivity and specificity of careHPV was 90.7% (95% CI 89.6-91.8) and 84.2% (95% CI 81.2-86.8), respectively. The agreement was similar in the stratified analyses where the kappa values were 0.75 (95% CI 0.70-0.79) in women aged 25-34, 0.66 (95% CI 0.62-0.70) in women aged 35-60, 0.73 (95% CI 0.70-0.77) at the Ocean Road Cancer Institute, 0.64 (95% CI 0.60-0.69) at the Kilimanjaro Christian Medical Center, 0.73 (95% CI 0.68-0.79) in HIV-positive and 0.66 (95% CI 0.63-0.70) in HIV-negative women. The kappa value of 0.64 (95% CI 0.39-0.88) for cervical high-grade lesions indicates a substantial agreement between careHPV and HC2 in detecting HPV among women with cervical high-grade lesions.

CONCLUSIONS

A substantial agreement was found between careHPV and HC2 in detecting HPV overall as well as detecting HPV among women with cervical high-grade lesions. However, given the limited resources available in low and middle-income countries, the HPV testing assay should be weighed against the cost-effectiveness of the test.

Evaluation of the effectiveness of high-risk human papilloma self-sampling test for cervical cancer screening in Bolivia

BACKGROUND

In Bolivia the incidence and mortality rates of uterine cervix cancer are the highest in America. The main factor contributing to this situation is the difficulty of establishing and maintaining quality prevention programs based on cytology. We aimed to evaluate the effectiveness of HR-HPV testing on self-collected samples to detect cervical intra-epithelial neoplasia and identify the best combination of screening tests.

METHODS

A total of 469 women, divided in two groups, were included in this study. The first group included 362 women that underwent three consecutively primary screening tests: self-collected sampling for HR-HPV detection, conventional cervical cytology and visual inspection under acetic acid (VIA). The second group included 107 women referred with a positive HR-HPV test that underwent conventional cervical cytology and VIA. The presence of high grade intraepithelial lesion (CIN 2+) or invasive cancer was verified by colposcopy and biopsy.

RESULT

In the screening group the sensitivity to detect high grade intraepithelial lesion (CIN 2+) or invasive cancer were 100, 76, 44% for the VIA, HR-HPV test and cytology, respectively. In the referred group, the sensitivity to detect high grade intraepithelial lesion (CIN 2+) or invasive cancer by VIA and cytology were 100 and 81%, respectively.

CONCLUSIONS

VIA and HR-HPV self-sampling were the best combination to detect CIN2+ lesions. Cytology analysis gave the poorest performance.