Human papillomavirus genotyping as a tool for cervical cancer prevention: from commercially available human papillomavirus DNA test to next-generation sequencing

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.

Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay

(1) Background: Human papillomaviruses (HPVs) are known to be related to the development of about 5% of all human cancers. The clinical relevance of HPV infection has been deeply investigated in carcinomas of the oropharyngeal area, uterine cervix, and anogenital area. To date, several different methods have been used for detecting HPV infection. The aim of the present study was to compare three different methods for the diagnosis of the presence of the HPV genome. (2) Methods: A total of 50 samples were analyzed. Twenty-five of them were tested using both next generation sequencing (NGS) and VisionArray® technology, the other 25 were tested using Hybrid Capture (HC) II assay and VisionArray® technology. (3) Results: A substantial agreement was obtained using NGS and VisionArray® (κ = 0.802), as well as between HC II and VisionArray® (κ = 0.606). In both analyses, the concordance increased if only high risk HPVs I(HR-HPVs) were considered as “positive”. (4) Conclusions: Our data highlighted the importance of technical choice in HPV characterization, which should be guided by the clinical aims, costs, starting material, and turnaround time for results.