Human Papillomavirus Genotyping Assay Research Articles

HPV genotyping in clinical samples using long-read single-molecule real-time sequencing.

Human papillomavirus (HPV) genotyping is widely used, particularly in combination with high-risk (HR) HPV tests for cervical cancer screening. We developed a genotyping method using sequences of approximately 800 bp in the E6/E7 region obtained by PacBio single molecule real-time sequencing (SMRT) and evaluated its performance against MY09-11 L1 sequencing and after the APTIMA HPV genotyping assay. The levels of concordance of PacBio E6/E7 SMRT sequencing with MY09-11 L1 sequencing and APTIMA HPV genotyping were 100% and 90.8%, respectively. The sensitivity of PacBio E6/EA7 SMRT was slightly greater than that of L1 sequencing and, as expected, lower than that of HR-HPV tests. In the context of cervical cancer screening, PacBio E6/E7 SMRT is then best used after a positive HPV test. PacBio E6/E7 SMRT genotyping is an attractive alternative for HR and LR-HPV genotyping of clinical samples. PacBio SMRT sequencing provides unbiased genotyping and can detect multiple HPV infections and haplotypes within a genotype.

Clinical performance of a newly developed domestic urine-based HPV test for cervical cancer screening in China.

Although urine-based human papillomavirus(HPV) detection is promising in cervical cancer screening, it has not yet been well-developed. Women aged 30-65 were invited to participate in the current study to provide one urine and two paired vaginal samples. Urine was detected by polymerase chain reaction(PCR)-based HPV test (urine-based HPV test). Two vaginal samples were tested by careHPV and GenPlex® HPV genotyping assay, respectively. Women with vaginal HPV positive were called back for colposcopy and biopsied if clinically indicated. The consistency was 79.0% (κ = 0.563) and 80.5% (κ = 0.605) between the urine-based HPV test, careHPV test, and GenPlex® HPV genotyping assay. Against CIN2detection, the careHPV test showed 77.4% sensitivity, and 71.0% specificity, while the GenPlex® HPV genotyping assay had a sensitivity of 100% and a specificity of 58.7%. For urine-based HPV test, the corresponding rates were 96.8% and 58.7%. Moreover, no significant differences were observed between the urine-based HPV test and careHPV test (p = 0.3395) and GenPlex® HPV genotyping assay (p = 0.338). The newly developed urine-based HPV test demonstrated acceptable consistency and comparable clinical performance with referenced HPV tests for vaginal samples. Therefore, urine-based HPV detection could be a useful alternative for women with difficulties to access cervical cancer screening.

Comparison of Urine and Genital Samples for Detecting Human Papillomavirus (HPV) in Clinical Patients.

Human papillomavirus (HPV) is the main cause of cervical cancer. The aim of the present study was to investigate HPV DNA detection and genotyping on paired genital and urine samples and to evaluate if urine samples could be used to monitor HPV infection. Study subjects were recruited from one local hospital in Guangdong of China from September 1, 2011, to June 30, 2012. They were invited to participate if they have taken an HPV genotyping assay for clinical diagnosis of the genital-urinary disease or for a health check-up 3-5 days ago. DNA was extracted from paired genital and urine samples; genotyping was performed with the GenoArray assay. A total of 250 patients were recruited, which included 203 females and 47 males. Our results showed that the overall agreement on HPV status between the paired samples was 77.1% (155/201, 95% CI: 0.713-0.829) for females, with a kappa value of 0.523 (95% CI: 0.469-0.632), while the agreement was extremely low in the paired male samples. As to individual genotyping, the greatest agreement was found for HPV16 type-specific identification in females (96.02%, 0.933-0.987), followed by the other 12 high oncogenic risk (HR-HPV) types, while the agreement for low-risk HPV detection is poor (κ < 0.6). Agreement between paired samples showed that HPV detection had a significantly greater concordance in the samples obtained in females than males (p = 0.002). Moreover, the agreement for low-risk HPV detection was significantly lower as compared to HR-HPV detection (48.1% vs. 62.3%, p = 0.044). Despite reduced sensitivity, HPV detection in urine closely represents the same trend that is seen with genital sampling. Urine appears to be an appropriate surrogate sample for HPV DNA detection in women with very limited access to healthcare, while the utility of urine for HPV DNA detection in males is less certain.

Pre-Vaccination Human Papillomavirus Genotypes and HPV16 Variants among Women Aged 25 Years or Less with Cervical Cancer.

In 2007, Australia introduced a national human papillomavirus (HPV) vaccination program. In 2017, the onset of cervical screening changed from 18 to 25 years of age, utilising human papillomavirus (HPV) nucleic acid testing. The objective of the study is to describe the HPV genotypes and HPV16 variants in biopsies from women ≤ 25 years of age with cervical carcinoma (CC) (cases), compared with those aged >25 years (controls), in a pre-vaccination cohort. HPV genotyping of archival paraffin blocks (n = 96) was performed using the INNO-LiPA HPV Genotyping assay. HPV16-positive samples were analysed for variants by type-specific PCR spanning L1, E2 and E6 regions. HPV16 was the commonest genotype in cases (54.5%, 12/22) and controls (66.7%, 46/69) (p = 0.30), followed by HPV18 (36.3%, 8/22 vs. 17.3% 12/69, respectively) (p = 0.08). Furthermore, 90% (20/22) of cases and 84.1% (58/69) of controls were positive for HPV16 or 18 (p = 0.42); 100% (22/22) of cases and 95.7% (66/69) of controls had at least one genotype targeted by the nonavalent vaccine (p = 0.3). The majority of HPV16 variants (87.3%, 48/55) were of European lineage. The proportion of unique nucleotide substitutions was significantly higher in cases (83.3%, 10/12) compared with controls (34.1%, 15/44), (p < 0.003, χ2, OR 9.7, 95%CI 1.7-97.7). Virological factors may account for the differences in CCs observed in younger compared with older women. All CCs in young women in this study had preventable 9vHPV types, which is important messaging for health provider adherence to new cervical screening guidelines.

Geotropism and oncogenic potential of HPV infections in cohort study populations in Vojvodina, North region of Serbia

Background/Aim: Geotropism of the human papillomavirus (HPV) represents the heterogeneous distribution of different genotypes worldwide. Aim of this study was to evaluate the prevalence of the HPV infection in women from Vojvodina, Serbia, according to cytological status and pathological changes of cervix - dysplasia and cancer. Methods: The research was conducted as a retrospective study at the Oncology Institute of Vojvodina and the Institute of Public Health of Vojvodina (IPHV). Data from the medical records of female patients treated for cervical intraepithelial neoplasia or cervical cancer at the Department of Gynaecology, Clinic for Surgical Oncology, Oncology Institute of Vojvodina in Sremska Kamenica in the period from 2016 to 2021 were used, as well as the laboratory findings of the IPHV for a group of patients with normal cytological results of the Papanikolau (PAPA) smear. Results: A total of 731 women, from 20 to 82 years of age, with different cytological results were enrolled. 567 samples were classified as NILM, while 164 samples belong to a group of abnormal histopathology (LSIL/HSIL/cervical cancer). The HPV genotyping assay was performed using the EUROArray HPV test to detect 30 HPV genotypes. In the overall number with normal cytological findings, HPV infection was verified in 242 (42.7 %) patients, of which 135 (55.8 %) were verified with high risk HPV, while 76 (31.4 %) were verified with a mixed group of HPV (Low risk/High risk HPV). Most prevalent genotypes were HPV 16, 31, 53, 51 and 18 in NILM cytological status. In the samples with the abnormal histopathology, the most prevalent genotypes were HPV 16, 33, 31 and 56, while 18 and 39 were equally verified. Genotype 16 was the most prevalent in the examined sample, with a higher prevalence in higher-grade histopathological findings: 18.8 % in LSIL, 31.9 % in HSIL and 75.0 % in cervical cancer samples. Infection with multiple associated genotypes of HPV was not correlated with histopathology. By comparing histopathological diagnosis and age, older patients had higher-grade lesions. Conclusion: Based on the estimated oncogenic potential of HPV genotypes as well as their prevalence in presented sample, it can be concluded that the nine-valent HPV vaccine for genotypes 6, 11, 16, 18, 31, 33, 45, 52 and 58 would have the potential to prevent HPV infection and the incidence of precancerous lesions and cervical cancer in about 85 % of women. Observing trends in the prevalence of HPV, especially HR HPV genotypes, can be important in the further strategy of applying secondary and primary prevention, as well as the application of HPV detection as part of co-testing or considering the introduction of HPV testing in the initial screening program.

Detection of Human Papilloma Virus (HPV) Infection in Colorectal Cancer and Viral Genome Integration Status

Background: Colorectal cancer (CRC) is the third common cause of malignancy in Iran, and its incidence rate has been raised due to an increase in individual and environmental risk factors. Objectives: The present study aimed to define the role of human papillomavirus (HPV) infection in CRC, then by drawing a phylogenetic tree, we aimed to analysis the sequences of isolated HPVs, and finally determine the viral genome physical status for HPV-16. Methods: A nested-PCR (nPCR), direct sequencing, and INNO-LiPA HPV genotyping assay were carried out for HPV detection, and a quantitative real-time PCR assay (qRT-PCR) was conducted for the physical status of the viral genome. Results: Among 157 subsets, there were 66 cases and 91 controls. Moreover, 5.7% (9/157) were HPV positive by nPCR, among whom 9.1% (6/66) were cases and 3.3% (3/91) were control groups (P = 0.750). The qRT-PCR analysis showed three forms of integrated, episomal, and mixed forms in our three HPV-16 strains. A higher rate of HPV infection was detected in the CRC cases; however, it was not statistically significant. Conclusions: Although there were limited positive results, higher ages (&gt; 65) were related to HPV involvement and CRC outcome. Furthermore, 9.1% of the CRC cases were infected with HPVs. The HPV-16 genome integration is observed in high-grade cancer cases with severe malignancy in CRC patients.

Long-term human papillomavirus vaccination effectiveness and immunity in Rwandan women living with and without HIV: a study protocol

IntroductionProphylactic human papillomavirus (HPV) vaccines have been shown to be highly effective in protecting women against cervical infections, high-grade abnormalities and cancer caused by the targeted HPV types. However, the...

Comparison of Seegene Anyplex II HPV28 assay with BD Onclarity HPV assay for human papillomavirus genotyping.

Presently, human papillomavirus (HPV)-based cervical cancer screening is commonly used and is replacing conventional cytology screening tests. The HPV genotyping assay is useful for triage in cervical cancer screening and the evaluation of HPV vaccination effects. In this study, we evaluated the clinical performance of two HPV genotyping assays, BD Onclarity HPV (Onclarity) and Seegene Anyplex II HPV28 (Anyplex) in the detection of relevant cervical lesions and for HPV genotyping concordance. Anyplex and Onclarity assays were performed on 920 consecutive liquid-based specimens. Anyplex, sensitivity, specificity, and genotyping concordance with Onclarity were optimal when restricted to ≥2+ (medium) viral loads. HPV genotyping agreement between the two assays ranged between 0.75 and 0.9 (excellent), except for HPV 33/58, which was 0.73 (good). With Onclarity as a reference, the relative sensitivity of Anyplex for the detection of ≥CIN 2 was 1.05 (95% CI: 0.99–1.1) and the relative specificity for detection of negative for intraepithelial lesion and malignancy (NILM) was 0.89 (95% CI: 0.85–0.93). For most ≥CIN 2 lesions, high-risk HPV was detected by Onclarity (66/72) and Anyplex (69/72) assays. For high-risk HPV negative ≥CIN 2 lesions, possible high-risk HPV genotypes were detected by Anyplex. In conclusion, the genotyping agreement between the tests was good to excellent. Full genotyping with Anyplex might confer additional benefits to patients with ≥CIN 2, although the difference is small. We also suggest an optimal cutoff value when reporting HPV infections using the Anyplex assay (≥2+; medium viral loads).

A Technical Comparison of Human Papillomavirus Genotyping Assays from a Population-Based Cervical Cancer Screening in South Central Ethiopia.

PurposeHigh-risk Human Papillomavirus (HPV) is the most important cause of cervical cancer. The highest burden of disease is seen in Low- and Low-Middle-Income Countries (LMIC). Several new HPV screening assays have been developed for high-risk HPV (hr-HPV) testing. We compared the performance and adequacy of three HPV genotyping assays on samples from a population of rural women in south-central Ethiopia.Patients and MethodsOne hundred and ten cervical swabs from rural women screened for HPV were assayed. HPV DNA was tested using MPG-Luminex Assay, Anyplex II HPV HR Detection, and EUROArray HPV. MPG-Luminex Assay was used as a reference method to compute the sensitivity and specificity of the two commercial assays in detecting hr-HPV infections.ResultsOf the 110 samples, MPG-Luminex Assay found 18.2% positive for the 14 hr-HPV and 7.3% for the probable hr-HPV genotypes. Anyplex™ II HPV HR Detection assay and EUROArray HPV Assay identified 21.82% and 12.7% samples, respectively, for the 14 hr-HPVs and both 7.3% for the probable hr-HPV genotypes (κ=0.734). Among the 14 hr-HPV genotypes, the genotype-specific agreement of the three HPV genotyping assays was moderate or better for HPV16, 31, 35, 39, 52, 56, 66 and 68. The aggregated sensitivity in detecting the 14 hr-HPV infections of Anyplex™ II HPV HR Detection and EUROArray HPV assays was high, 100% and 70%, respectively. The specificities of Anyplex™ II HPV HR Detection and EUROArray HPV were 95.6% and 100%, respectively.ConclusionThe three evaluated assays showed similar analytical performance in the detection of hr-HPV infections and moderate or better concordance in HPV genotyping. This study is part of the ongoing cluster-randomized trial that has been registered in clinicaltrials.gov (NCT03281135) on September 13, 2017.

Human Papillomavirus and Risk of Head and Neck Squamous Cell Carcinoma in Iran.

ABSTRACTHuman papillomavirus (HPV) causes a subset of head and neck squamous cell carcinoma (HNSCC). Knowledge of determinants of α-, β-, and γ-HPVs types in the oral cavity is required for a better understanding of HNSCC development. Oral rinse samples of 498 HNSCC cases and 242 controls from the IROPICAN study—a large multicenter case-control study in Iran—were screened for 21 α-HPV, 46 β-HPVs, and 52 γ-HPVs using bead-based HPV genotyping assays. α-HPVs were detected only in 1.2% of the patients and 2.9% of the controls from which HPV16 was the most prevalent type among participants. β-HPVs were detected in 43.8% of the patients and 38.6% of the controls where the lip and oral cavity (45.5%) had the highest positivity. Values for γ-HPV prevalence in patients and controls were 26.1% and 24.7%, respectively. The highest percentage of γ-HPV positivity was found in the larynx (30.4%). Concerning the β genus, HPV23 and HPV38 were the most prevalent types among the patients and controls, respectively. For the γ genus, SD2 in cases and HPV134 in controls were the most prevalent types. Overall, detection of α-HPVs (aOR, 0.40; 95% CI = 0.1 to 1.2; P = 0.11), β-HPVs (aOR, 1.9; 95% CI = 0.9 to 1.6; P = 0.29), and γ-HPVs infections (aOR, 1.04; 95% CI = 0.7 to 1.5; P = 0.83) was not associated with the HNSCC development. Our data did not suggest an HPV-related etiology for HNSCC pathogenesis. Nonetheless, this study provides novel insights into the diversity of β-, and γ-HPVs in different HNSCC anatomical subsites.IMPORTANCE Infection with human papillomavirus (HPV) is responsible for a subset of neck squamous cell carcinoma (HNSCC), but knowledge of the prevalence of and risk factors for oral HPV infection, especially cutaneous types in Iran, remains unknown. In a large retrospective study, the authors used a sensitive assay for the detection of α-, β-, and γ-HPVs in oral rinse samples of HNSCC and matched controls. They find that the α-HPV contribution to HNSCC in Iran is lower than global prevalence. High-risk α-HPVs or cutaneous β- and γ-HPVs were not associated with the HNSCC development. Besides, this study provides novel insights into the diversity of β- and γ-HPVs in different HNSCC anatomical subsites.

Detection accuracy of the Cobas HPV assay for high-risk HPV in head and neck FNA biopsy specimens.

This study evaluated the detection accuracy of the Cobas human papillomavirus (HPV) assay for high-risk human papillomavirus (hrHPV) and HPV-16 in head and neck fine-needle aspiration (FNA) specimens with squamous cell carcinoma. Head and neck FNA biopsy specimens from 2012 to 2020 were retrospectively collected. Cobas HPV testing was performed on 90 FNA specimens with valid Cervista HPV testing results. Results of Cobas HPV and Cervista HPV assays were compared. A Linear Array or SPF10-LiPA25 HPV genotyping assay resolved cases with discrepant results. The κ value and accuracy of Cobas HPV testing were calculated. The accuracy of the Cobas HPV assay was also determined in 42 FNA needle-rinse specimens. Cobas HPV was positive in 82% of the FNA specimens (74 of 90). The concordance between Cobas HPV and Cervista HPV test results was 88.9% (80 of 90) with substantial agreement (κ = 0.669; 95% CI, 0.481-0.856). With HPV genotyping confirmation in cases with discrepant results between the 2 HPV assays, Cobas HPV showed 100% sensitivity and specificity for hrHPV. HPV-16 was detected in 88% of HPV-positive cases (65 of 74). HPV genotyping confirmed 1 false-negative HPV-16 result and 1 false-positive HPV-16 result. Overall, the accuracy of Cobas HPV for HPV-16 was 97.8%. The accuracy of Cobas HPV in FNA needle-rinse specimens was 100%. The Cobas HPV assay is highly accurate for determining the HPV status in head and neck FNA specimens. FNA needle rinse is valid for Cobas HPV testing in patients with squamous cell carcinoma.

Abstract 363: Investigating the potential clinical predictive value of virus genotype, menopausal status and mutational landscape in cervical cancer tissue using a NGS based human papillomavirus (HPV) assay and whole exome sequencing (WES)

Abstract Purpose: Persistent HPV infections are associated with nearly all cervical cancers and some head &amp; neck and genitourinary cancers. In cervical cancer, 14 high risk HPV genotypes have been previously identified with varying geographical prevalence and carcinogenicity. HPV16 and 18 account for &amp;gt;70% of cervical cancer incidence worldwide. There is an unmet need to explore HPV-associated cancer pathology, HPV infection status and molecular profiles to detect virus load and identify predictive gene signatures. We investigated the association between HPV genotypes and clinicopathological features and analyzed the mutational landscape using the ImmunoID NeXT Platform®. Methods: Early stage cervical cancer FFPE tissue samples (n=38) were analyzed. We detected and quantified oncoviral DNA, identified likely somatic mutations, and quantified genome-wide mutational burden. Any sample with at least one filtered read of HPV evidence was considered positive; zero such evidential reads were reported across a negative control cohort of &amp;gt; 439 non-cervical cancer samples. Oncovirus DNA counts and HPV genotype status were then evaluated against covariates (age; menopausal status) for statistical significance. Finally, mutation frequency was assessed in genes comprising major cervical cancer driver pathways from the KEGG and Biocarta databases. Results: Oncoviral HPV infections were detected using a NGS based approach in all tumor tissue with demonstrated robust assay performance. A statistically significant difference in viral DNA counts was observed between high risk genotypes HPV16 and 18 (n=27) and all other genotypes (n=10), (p=0.028, Student's t). Genotypes were also significantly associated with menopausal status (p=0.01, Fisher's Exact Test) and age at surgical resection (p=0.011, Student's t). Among the pathways considered, TGF-β and MAP-kinase were the most frequently mutated across 38 samples and multiple pathway annotations. Conclusions: We applied a powerful NGS based WES approach that enables accurate detection of HPV genotypes with quantification of HPV viral DNA. This quantitative approach represents a possible promising clinical benefit over existing qualitative HPV genotyping assays and may have the potential for further development to define cancer type and treatment specific cutoff values for cancer prognosis. Furthermore, our results demonstrate that a WES based approach provides clinically valuable insights into the constitutive molecular mechanisms of cervical cancer. The association of HPV genotypes with clinical patient characteristics and/or mutational profiles has the potential to identify prognostic and predictive clinical biomarkers and to provide critical information for treatment defining strategies. Citation Format: Jean-Christophe Pignon, Heidi Giese, Dorothee Foernzler, Lee D. McDaniel, Gabor Bartha, Juergen Scheuenpflug, Zheng Feng. Investigating the potential clinical predictive value of virus genotype, menopausal status and mutational landscape in cervical cancer tissue using a NGS based human papillomavirus (HPV) assay and whole exome sequencing (WES) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 363.

High human papillomavirus prevalence among females attending high school in the Eastern Cape Province of South Africa.

As part of the human papillomavirus (HPV) vaccination strategy in South Africa, it is essential to have information on HPV prevalence, and HPV types distribution among the unvaccinated population. Information on the prevalence of HPV and the distribution of HPV types in adolescents and young women in South Africa’s Eastern Cape Province is minimal. Therefore, this study investigates the prevalence, distribution of HPV types, and factors associated with HPV infection amongst unvaccinated female learners. A sample composed of 213 sexually active female learners attending high schools in the Eastern Cape Province of South Africa; median age 18 years, who provided self-collected vaginal specimens. Roche Linear Array HPV genotyping assay that detects 37 HPV genotypes was used to detect HPV infection. HPV infection was detected in 76.06% (162/213) of participants. Of these 14.55% (31/213) were positive for HPV types targeted by the Cervarix® HPV vaccine (HPV-16 and/or 18), 20.66% (44/213) by Gardasil®4 (HPV-6, -11, -16 and/or -18) and 37.09% (79/213) by Gardasil®9 (HPV-6, -11, -16, -18, -31, -33, -45, -52 and/or -58). HPV-35, commonly detected in cervical cancer cases among women of African ancestry, was frequently detected (9.40%). Participants who reported to have ever consumed alcohol had a significantly higher risk of HPV infection (OR: 2.91, 95% CI: 1.38–6.11, p = 0.005). High HPV prevalence was observed among participants. The high prevalence of HPV types targeted by the Gardasil®9 vaccine encourages the introduction of the Gardasil®9 vaccine. Data from this study will inform both vaccination campaigns and monitor the impact on HPV types after vaccination.

Development and validation of a wart-associated human papilloma virus genotyping assay for detection of HPV in cutaneous warts.

Cutaneous warts are infectious disorders caused by human papillomavirus (HPV). A recent study revealed that the HPV genotype influences the natural course and response to treatment for plantar warts, suggesting that HPV genotyping could potentially be used to optimize wart treatment schemes. For this purpose, a wart-associated HPV genotyping assay was developed. The assay was subjected to an intensive validation process including, i.a., empiric determination of the annealing temperature, primer-probe optimization, evaluation of the analytical specificity and sensitivity, viral load quantification, and qualitative as well as quantitative analysis of intra-run repeatability and inter-run reproducibility. The newly developed assay was employed in a small-scale HPV genotyping study of wart biopsies (n = 50). The assay exhibited an analytical type-specific sensitivity and specificity of 100% (95% confidence interval [CI]: 83.9%-100%). The limit of quantification of the tested sequences corresponded to less than 17 viral copies/µl, while the limit of detection was less than 5 copies/µl. Very good to excellent agreements were gained between intra- and inter-run measurements (κ = 0.85-1.00) and coefficients of variation of the quantitative agreements were less then 3%. 22.5% (95% CI: 11%-39%) of the analyzed biopsies were negative for the tested HPV types, while 35% (95% CI: 21%-52%) contained multiple infections. The wart-associated HPV quantitative polymerase chain reaction assay was proven to be highly sensitive and specific. Multiple HPV infections were detected in 35% of lesions, contradicting the current literature claiming that in immunocompetent patients only 4%-16% of warts exhibit multiple HPV infections. This assay is qualified to be implemented in development of future genotype specific wart treatment strategies.

Cross comparison of AmpFire HPV genotyping assay and Roche human papillomavirus (HPV) linear array for HPV genotyping of anal swab samples

Although anal cancers represent just 0.5 % of all new cancer cases in U.S., rates have increased markedly, with highest rates in HIV-infected MSM. American Cancer Society estimates there will be ∼9090 new cases and ∼1420 deaths in 2021. We compared Roche Linear Array HPV Genotyping (Roche) and AmpFire HPV Genotyping (AmpFire) assays for concordance and agreement to detect 15 hr-HPV types from 151 anal specimens. Within run precision of AmpFire was assessed on 50 anal specimens. Specimens with Roche Combo-positive and HPV33, HPV35 and/or HPV58-positive results were further tested using HPV52-specific TaqMan assay. AmpFire generated valid results on 149/151 (98.7 %) specimens; 135/149 (90.6 %) and 134/149 (89.9 %) had detectable HR-HPV DNA by AmpFire or Roche, respectively. Overall concordance was 89.8 % (2007/2235, κ = 0.65). HPV16 showed highest overall concordance at 93.3 % (139/149, κ = 0.84). HPV68 had lowest overall concordance at 77.2 % (115/149, κ = 0.28). Kappa values were interpreted as being moderate or good for all other HR-HPV types. Within run precision generated 744/750 concordant results; R2 value = 0.97 (p < 0.0001) (Mantel Test). In conclusion, AmpFire and Roche demonstrated good inter-assay agreement for detecting most HR-HPV types from anal samples, with AmpFire detecting a broader range of HPV68 subtypes and detecting HPV52 without the need for confirmatory testing.

Clinical Significance of the Interaction between Human Papillomavirus (HPV) Type 16 and Other High-Risk Human Papillomaviruses in Women with Cervical Intraepithelial Neoplasia (CIN) and Invasive Cervical Cancer.

The aim is to evaluate the clinical consequences of coinfection between HPV 16 and other high-risk HPVs among women with a histological diagnosis of CIN or invasive cervical cancer. A total of 2985 women, with a diagnosis of either CIN or cancer (<IB) on cervical or cone biopsy, were included. HPV genotypes were identified using the INNO-LiPA HPV genotyping assay, version EXTRA, on cervical scraping, before the colposcopic evaluation and the colposcopic biopsies or conization. In the overall population, HPV16 interacted positively with HPV18 (RR = 2, 95% CI 1.5–2.6) and negatively with HPV33, 51, 52, and 66, in log-linear analysis. There was an excess of CIN3 diagnoses among subjects coinfected with HPV16 and HPV18 or HPV52, although the absolute number of cases was relatively small. In a logistic model, the odds ratio of CIN3+ associated with coinfection of HPV16 and HPV18 (OR = 3.8, 95% CI 2.5–5.7, p=0.004 compared to single HPV16) or HPV52 (OR = 3.6, 95% CI 2.6–5.1, p=0.009 compared to single HPV) was higher than that associated with single HPV 16 infections. Finally, multiple infections had no effect on residual disease and did not influence the recurrence of high-grade CIN during a median follow-up of 25 months (IR 17–41). HPV16 interacted positively with HPV18 and negatively with HPV33, 51, 52, and 66 supporting the notion that HPV16 interacts mostly negatively with other HR-HPVs in CIN lesions. Among specimens coinfected with HPV16 and 18 or 52, there was an excess of CIN3+ although the impact on the prevalence of severe cervical lesions was limited.

The relationship of human papillomavirus infection with endocervical glandular involvement on cone specimens in women with cervical intraepithelial neoplasia

ObjectiveThe aim of study was to evaluate the association of endocervical gland involvement (EGI) on histological samples with high risk (HR) human papillomavirus (HPV) infection and with the persistence/recurrence rate of cervical intraepithelial neoplasia (CIN) after treatment. MethodsA total of 1301 subjects who had conization procedures after cervical punch biopsies (533 persistent CIN1, 768 CIN2+ including 20 microinvasive cervical cancer) were enrolled in the study. HPV genotypes were identified using the INNO-LiPA HPV genotyping assay on cervical scraping. Logistic regression and Cox regression analyses were used to evaluate the association of EGI on the persistence/recurrence rate of CIN after treatment. ResultsThe rate of EGI on final histology was 46.3% (602/1301). HPV 16 was the only HR-HPV significantly associated with increasing rates of EGI (231/602 as compared to 211/699, p = 0.002). EGI was also associated with an excess of multiple HR-HPV infections (237/602 as compared with 225/699, p = 0.006). After correction for confounders, the odds ratio of EGI among women infected by HPV 16 was 1.41 (95% CI = 1.12–178). CIN2+ lesions were diagnosed in 40.5% (283/699) of EGI negative subjects and 86.7% (522/602, p < 0.001 compared to negative subjects) of EGI positive subjects.After a median of 25 months of follow-up (IQR = 15–47) of 1090 treated women, the persistence of HPV 16 during follow-up was 38.1% (93/217, p = 0.03 compared to EGI negative) among EGI positive and 32% (58/181) among controls. After corrections for potential confounders, the odds ratio of CIN2+ persistence and or recurrence was higher among EGI positive (OR = 2.35, 95% CI = 1.16–4.77) than negative controls. ConclusionEGI on histological samples is associated with increased rates of HPV 16, multiple high risk-HPV infections and CIN2+ lesions. EGI positive subjects also had an increased CIN recurrence/persistence after treatment compared to controls.

The Triage Effectiveness of an Extended High-Risk Human Papillomavirus Genotyping Assay for Women with Cytology Showing Atypical Squamous Cells of Undetermined Significance in China.

PurposeLittle is known about the performance of extended high-risk human papillomavirus (HR-HPV) genotyping triage of cytology showing atypical squamous cells of undetermined significance (ASC-US). This study aims to evaluate the effectiveness of triage with different HR-HPV genotype models among women with ASC-US.Materials and MethodsIn this study, all women who underwent cervical cytology and HR-HPV genotyping were enrolled from 2014 to 2017 in China, and those with cytology showing ASC-US were referred for colposcopy and/or biopsy. The endpoint was histological detection of cervical intraepithelial neoplasia grade 2 or worse (CIN2+). The outcome indicators were the sensitivity, specificity, positive predictive values (PPVs), negative predictive values (NPVs) and colposcopy referral rates.ResultsIn all, 56,788 women were enrolled in this study, and 2658 (4.97%) women were reported to have ASC-US; 10.1% (242/2393) of women with ASC-US were identified as having CIN2+. The HR-HPV infection rate was 95.0% among all women with ASC-US who were identified as CIN2+, and the top five genotypes with prevalence and risk of CIN2+ were HPV16 (OR=26.38), HPV58 (OR=7.04), HPV18 (OR=4.44), HPV33 (OR=3.38), HPV31 (OR=2.97) and HPV52 (OR=2.96). The HPV16/18/31/33/52/58 model achieved higher sensitivity [91.3 (87.8–94.9)], specificity [70.0 (68.1–72.0)], PPV [25.5 (22.4–28.2)] and NPV [98.6 (97.3–98.7)] for the triage of ASC-US patients than the other HR-HPV-type combination models, but the colposcopy referral rate (36.2%) was significantly lower than that of the recommended HR-HPV nongenotyping model (47.6%).ConclusionThis study confirms that the specific HR-HPV genotype HPV16/18/31/33/52/58 is an alternative strategy for ASC-US triage and can effectively reduce the high burden of colposcopy referrals in China.

Human Papillomavirus (HPV) Genotyping Assay Suitable for Monitoring the Impact of the 9-Valent HPV Vaccine.

In Japan, a bivalent human papillomavirus (HPV) vaccine against carcinogenic HPV16/18 was licensed in 2009, and a quadrivalent vaccines against HPV16/18 and non-carcinogenic HPV6/11 was licensed in 2011. Recently, the next-generation 9-valent vaccine targeting HPV6/11/16/18/31/33/45/52/58 has been approved. Accurate HPV genotyping is essential for HPV vaccine research and surveillance. The Roche Linear Array (LA) has long been a standard assay for HPV genotyping, but its recent product discontinuation notice has urged us to introduce an alternative assay with comparable performance. In the present study, an in-house HPV genotyping assay that employs PCR with PGMY09/11 primers and reverse blotting hybridization (PGMY-CHUV) was compared with LA to assess genotype-specific agreement. A total of 100 cervical precancer specimens were subjected to both PGMY-CHUV and LA. For detection of genotypes included in the 9-valent vaccine, PGMY-CHUV completely agreed with LA for detection of HPV6, HPV11, HPV16, HPV18, HPV33 and HPV45, and showed near-complete agreement for HPV31 and HPV58 (98% and 99%, respectively). Moreover, PGMY-CHUV detected a significantly higher prevalence of HPV52 than LA (22% vs. 14%, P = 0.008 by McNemar's exact test), with 92.0% overall agreement, 63.6% positive agreement and a kappa value of 0.73. Most (87.5%) of HPV52 discordant cases involved mixed infections with HPV35 or HPV58. In conclusion, while the two assays present equivalent data for assessing the effectiveness of the bivalent and quadrivalent vaccines, PGMY-CHUV is more suitable for evaluating the impact of the current 9-valent vaccine because of its superior detection of HPV52 in co-infection cases.

Genotyping of Human Papillomavirus in Cervical Squamous Intraepithelial Lesions in Mexican Women.

Approximately 40 genotypes of the human papillomavirus (HPV) have been identified in cervical mucosa. In particular, HPV-16 and HPV-18 have been associated with cervical neoplasia. Squamous intraepithelial lesions (SILs) are precursors of cervical cancer. This study aimed to identify the HPV by genotype in SILs using a linear array genotyping test in a population in Mexico. We performed a cross-sectional study of 129 female patients with or without SILs, as determined by colposcopy, who completed a risk factor questionnaire. Cervical swab samples were obtained and genotyped using a Linear Array HPV Genotyping assay. Forty-nine (37.98%) samples were positive for HPV, and 24 genotypes were identified among these samples. The most common genotype was HPV-16. Twelve genotypes were found in both high- and low-grade SILs (HPV-6, 16, 31, 39, 51, 52, 53, 58, 59, 61, 67, and 84), of which seven were high-risk SILs (HPV-16, 31, 39, 51, 52, 58, and 59). Among the populations studied, the most frequent genotype was HPV-16, multiple infections were found, and four patients without injury tested positive for HPV.