Comparison of the Cobas 4800 HPV and HPV 9G DNA Chip Tests for Detection of High-Risk Human Papillomavirus in Cervical Specimens of Women with Consecutive Positive HPV Tests But Negative Pap Smears

The analysis of HPV integration sites based on nanopore sequencing and the profiling changes along the course of photodynamic therapy

OBJECTIVE

To detect the HPV genotype and integration sites in patients with high-risk HPV infection at different stages of photodynamic therapy using nanopore technology and to evaluate the treatment effect.

METHODS

Four patients with HPV infection were selected and subjected to photodynamic therapy, and cervical exfoliated cell was sampled at before treatment, after three courses of treatment and six courses of treatment, their viral abundance and insertion sites were analyzed by nanopore technology, and pathological examinations were performed before and after treatment. In this study, we developed a novel assay that combined viral sequence enrichment and Nanopore sequencing for identification of HPV genotype and integration sites at once. The assay has obvious advantages over qPCR or NGS-based methods, as it has better sensitivity after viral sequences enrichment and can generate long-reads (kb to Mb) for better detection rate of structure variations, moreover, fast turn-around time for real-time viral sequencing and analysis.

RESULTS

The pathological grade was reduced in all four patients after photodynamic therapy. Virus has been cleared in two cases after treatment, the virus amount reduced after treatment but not completely cleared in one case, and two type viruses were cleared and one type virus persisted after treatment in the last patient with multiple infection. Viral abundance and the number of integration sites were positively correlated. Gene enrichment analysis showed complete viral clearance in 1 patient and 3 patients required follow-up.

CONCLUSION

Nanopore sequencing can effectively monitor the abundance of HPV viruses and integration sites to show the presence status of viruses, and combined with the results of gene enrichment analysis, the treatment effect can be dynamically assessed.

The Risk Factors for Cervical Cytological Abnormalities Among Women Infected With Non-16/18 High-Risk Human Papillomavirus: Cross-sectional Study

BACKGROUND

High-risk human papillomavirus (hrHPV) infection is a necessary cause of almost all cervical cancers. Relative to hrHPV 16/18 infection, non-16/18 hrHPV infection is of less concern. However, the increasing prevalence of non-16/18 hrHPV infections has become an important public health issue. The early identification and treatment of cervical cytological abnormalities in women infected with non-16/18 hrHPV reduces the incidence of cervical cancer. To date, no study has examined the risk factors for cytological abnormalities in this high-risk population.

OBJECTIVE

This population-based, cross-sectional study aimed to identify the risk factors for cervical cytological abnormalities in women infected with non-16/18 hrHPV.

METHODS

A total of 314,587 women from the general population were recruited for cervical cancer screening at 136 primary care hospitals in Xiangyang, China. Of these, 311,604 women underwent HPV genotyping, and 17,523 non-16/18 hrHPV-positive women were referred for cytological screening according to the screening program. A logistic regression model was used to assess the risk factors for cytological abnormalities among these non-16/18 hrHPV-positive women. A separate analysis was performed to determine the factors influencing high-grade cytological abnormalities.

RESULTS

The non-16/18 hrHPV infection rate was 5.88% (18,323/311,604), which was 3-fold higher than that of hrHPV 16/18 (6068/311,604, 1.95%). Among the non-16/18 hrHPV-positive women who underwent ThinPrep cytologic test, the overall prevalence rates of cervical cytological abnormalities and high-grade cytological abnormalities were 13.46% (2359/17,523) and 1.18% (206/17,523), respectively. Multivariate logistic regression analysis revealed that women with middle or high school educational attainment were at a higher risk of having cytological abnormalities than those who received primary education (odds ratio [OR] 1.31, 95% CI 1.17-1.45; P<.001, and OR 1.32, 95% CI 1.14-1.53; P<.001, respectively). Living in rural areas (OR 2.58, 95% CI 2.29-2.90; P<.001), gravidity ≥3 (OR 2.77, 95% CI 1.19-6.45; P=.02), cervix abnormalities detected in pelvic examination (OR 1.22, 95% CI 1.11-1.34; P<.001), and having a cervical cancer screening 3 years ago (OR 0.79, 95% CI 0.62-1.00; P=.048) were associated with cytological abnormalities. The risk factors for high-grade cytological abnormalities included middle school education (OR 1.45, 95% CI 1.07-1.98; P=.02), living in rural regions (OR 1.52, 95% CI 1.10-2.10; P=.01), and cervix abnormality (OR 1.72, 95% CI 1.30-2.26; P<.001).

CONCLUSIONS

The dominant epidemic of non-16/18 hrHPV infection is revealed in Chinese women. Multiple risk factors for cervical cytological abnormalities have been identified in women infected with non-16/18 hrHPV. These findings can provide important information for clinically actionable decisions for the screening, early diagnosis, intervention, and prevention of cervical cancer in non-16/18 hrHPV-positive women.

Comparison of the performance of HPV DNA chip test and HPV PCR test in cervical cancer screening in rural China

BACKGROUND

This study aimed to evaluate the performance of two different principles of HPV testing in primary cervical cancer screening and ASC-US triage in rural areas.

METHODS

3,328 and 3,913 women were enrolled in Shanxi, China in 2017 and 2018, respectively, and screened using liquid-based cytology and different HPV tests with a 4-year follow-up. Different screening methods commonly used in clinical practice were evaluated.

RESULTS

In the HPV PCR test cohort, the prevalence of HPV infection was 14.90%. A total of 38 cases of CIN2+ were identified at baseline, 2 of which were in the HPV-negative cohort and the rest in the HPV-positive cohort (2 = 186.85, p < 0.001). Fifty-three cases of CIN2+ were accumulated over 4 years. The HPV infection rate in the HPV DNA chip test cohort was 21.10%. A total of 26 CIN2+ cases were identified at baseline, all in the HPV-positive population (2 = 92.96, p < 0.001). 54 CIN2+ cases were cumulative over 4 years. At 4-year follow-up, HPV-negative results were significantly more protective against cervical intraepithelial neoplasia grade 2 or worse (CIN2+) than normal cytologic results at baseline. HPV screening was more sensitive and specific than cytologic screening (using ASC-US as the threshold) and performed better on the HPV DNA microarray test. In addition, compared with HPV 16/18 testing, sensitivity increases and specificity decreases when using HPV testing for cytologic ASC-US triage, regardless of which HPV test is used.

CONCLUSION

In the rural areas where we implemented the study, HPV tests performed well for screening than LBC and HPV DNA chip testing performed better than HPV PCR testing in the screening cohort. Optimal screening was achieved technically when used in combination with LBC for ASC-US population triage, without thinking the feasibility for resource availability.

NanoString Technology for Human Papillomavirus Typing

High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter^® platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 HPV types and the globin gene. We tested residual DNA extracts from epidemiologic specimens and defined samples (HPV plasmids at 10 to 10⁴ copies/reaction) directly (No-PCR) as well as after L1 consensus PCR of 45 (PCR-45) or 15 cycles (PCR-15). Assay and interpretation followed NS recommendations. We evaluated analytic performance by comparing NanoString results for types included in prior assays: Roche Linear Array (LA) or HPV TypeSeq assay. No-PCR results on 40 samples showed good type-specific agreement with LA (k = 0.621) but sensitivity was 65% with lower limit of detection (LOD) at 10⁴ plasmid copies. PCR-45 results showed almost perfect type-specific agreement with LA (k = 0.862), 82% sensitivity and LOD at 10 copies. PCR-15 results on 75 samples showed substantial type-specific agreement with LA (k = 0.796, 92% sensitivity) and TypeSeq (k = 0.777, 87% sensitivity), and LOD at 10 copies of plasmids. This proof-of-principle study demonstrates the efficacy of the NS platform with HPV CodeSet for type-specific detection using a low number of PCR cycles (PCR-15). Studies are in progress to evaluate assay reproducibility and analytic validation with a larger number of samples.

The clinical performance of human papillomavirus genotyping using PANArray HPV chip: Comparison to ThinPrep cytology alone and co-testing

Recently, a high-risk human papillomavirus (HR-HPV) detecting assay alone could be used as a first-line screening tool for cervical cancer, although the test system has been limited to the Cobas 4800 HPV test. However, the screening efficiency of the HPV chip, which is widely used in Eastern Asia because of the high prevalence of non16/18 HR-HPV genotypes, has not been well elucidated. After selecting 300 women who were co-tested using the PANArray HPV chip and the ThinPrep assay and had confirmed histological diagnoses, we evaluated the diagnostic accuracy of the PANArray HPV test based on direct sequencing and clinical performance compared to the ThinPrep alone and co-testing. HR-HPVs were identified in 212 (70.7 %) patients by the PANArray HPV test. The results of the PANArray HPV test and direct sequencing for detecting HR-HPVs were in almost perfect agreement, consistent in 95.3 % of the cases (k = 0.89). HR-HPVs were more commonly detected by the PANArray HPV assay in patients with high-grade squamous intraepithelial lesions (HSILs) or worse (p < 0.001, both) by cytological and histological examinations. The PANArray HPV test had higher sensitivity (91.7 %) than the ThinPrep (52.6 %) but co-testing increased the sensitivity for predicting HSIL or worse cervical lesions to 99.2 %. In conclusion, the PANArray HPV test accurately detected HR-HPVs determined by cytological and histological examinations to be HSIL or worse cervical lesions. The PANArray HPV assay alone was more sensitive than the ThinPrep alone for detecting HSIL or worse cervical lesions, however, co-testing enhanced the sensitivity. Co-testing is more useful for screening HSIL or worse lesions than use of either the ThinPrep or PANArray HPV genotyping alone.

PCR-reverse dot blot human papillomavirus genotyping as a primary screening test for cervical cancer in a hospital-based cohort

OBJECTIVE

To evaluate the polymerase chain reaction (PCR)-reverse-dot-blot (RDB) human papillomavirus (HPV) genotyping test as a feasible assay for the cervical cancer primary screening.

METHODS

In a hospital-based cohort, a total of 21,568 women were voluntarily enrolled from March 2009 to November 2016 for evaluating the 3 current cervical cancer screening strategies: co-test, cytology primary and high-risk HPV (HR-HPV) primary by using PCR-RDB HPV genotyping and liquid-based cytology (thinprep cytologic test [TCT]). Women with HR-HPV infection and/or abnormal cytology were referred for colposcopy, and the biopsy or conization was performed according to the American Society for Colposcopy and Cervical Pathology (ASCCP) guidelines.

RESULTS

Overall, 18.20% (3,935/21,568) of the women were detected as HR-HPV-positive, 5.04% (1,088/21,568) were diagnosed with cervical intraepithelial neoplasia 2 or higher (CIN2+), and 3.43% (739/21,568) with CIN3+. The cumulative incidence rates for CIN2+/CIN3+ in patients with HPV-16/18-positive were 48.28%/37.20%, while they were 0.86%/0.38%, 0.30%/0.15% and 0.18%/0.09% in cytology-negative, HR-HPV-negative and co-test-negative population, respectively. Using CIN2+ and CIN3+ as the observed endpoints, the sensitivity and negative predictive value (NPV) of HR-HPV genotyping as a primary screening tool were 90.99%/99.49% and 91.57%/99.80%. Moreover, using HR-HPV genotyping primary screening could detect the same more CIN2+/CIN3+ cases in baseline-detection as co-testing (990/700 vs. 991/701) and far more than cytology primary screening (903/656, p<0.05). It also achieved the lowest misdiagnosis rate (8.01%/5.02%). Although HPV genotyping primary screening required an increased number of colposcopies (2.75/3.89 per CIN2+/CIN3+ case), it yielded an acceptable rate.

CONCLUSIONS

The PCR-RDB HPV genotyping test is a cost-effective and beneficial cervical cancer primary screening for hospital-based opportunistic screening.

Analytic performance of PANArray HPV and HPV 9G DNA chip tests for genotyping of high-risk human papillomavirus in cervical ThinPrep PreservCyt samples

The detection of high-risk human papillomavirus (HR-HPV) is important for early diagnosis of precancerous cervical lesion. The distribution of HR-HPV genotypes in East Asia is different from that in Western countries. HR-HPVs non-16/18 including HPV-58 are highly prevalent in East Asia. Thus, a variety of HPV tests that could identify individual genotypes have been widely used. HPV 9G DNA is a deoxyribonucleic acid-based chip test, while PANArray HPV chip is a peptide nucleic acid-based array. We compared the analytic performance of these two chips for detecting and genotyping HR-HPV using 356 liquid-based cytology specimens and evaluated their diagnostic accuracies based on direct sequencing. For identifying HR-HPV, PANArray HPV and HPV 9G DNA chips agreed with each other for 85.1% of samples. Overall strength of agreement between the two tests was substantial (k = 0.68). Specifically, these two tests almost perfectly agreed for detecting several types of HR-HPV, including HPV-16, -18, -35, -52, -58, and -59 (k>0.81 for all). According to direct sequencing, PANArray HPV produced consistently higher sensitivities for detecting HR-HPV than HPV 9G DNA for either overall or individual genotypes of HR-HPV. Sensitivities and specificities for detecting HPV-58 were perfect (100%) with PANArray HPV. In conclusion, PANArray HPV is more effective than HPV 9G DNA in detecting HR-HPV. It is more useful for regions with high prevalent HPV-58 infection.

Prevalence of HPV-16/18 genotypes and immediate histopathologic correlation results in a Chinese population with negative cytology and positive high-risk HPV testing

BACKGROUND

The objective of this study was to examine the prevalence of human papillomavirus 16/18 (HPV-16/18) genotypes and immediate histopathologic correlations in a Chinese population with negative cytology and positive high-risk human papillomavirus (hrHPV) testing.

METHODS

Patients who had documented negative cytology with immediate follow-up (within the 6 months after negative for intraepithelial lesion or malignancy Papanicolaou [Pap] testing), including a histopathologic examination and/or hrHPV testing, between 2011 and 2018 were included, and the data were analyzed.

RESULTS

Among 1,424,182 Pap tests, 1,333,453 (93.6%) were interpreted as negative cytology. Although conventional Pap smears had the highest reporting rate, cervical intraepithelial neoplasia 2 and higher (CIN-2+) lesions were detected significantly more with liquid-based cytology preparations (2.1%) than the conventional method (1.4%; P < .01). The overall hrHPV-positive rate was 14.9% (25,507 of 171,273) in the women with negative cytology. Among the 18,423 cytology-negative, HPV-positive cases tested with the Cobas assay, the overall HPV-16/18 prevalence was 24.7%, with 17.9% being HPV-16-positive, 6.2% being HPV-18-positive, and 0.6% being positive for both HPV-16 and HPV-18. The immediate histopathologic examination was documented for 21,796 women with cotesting results, including 8915 HPV-positive cases and 12,881 HPV-negative cases. CIN-2+ lesions were diagnosed in 15.2% of the HPV-16-positive cases; this rate was significantly higher than the rates seen in the HPV-18-positive cases (4.8%) and the cases positive for 1 of the other 12 types of HPV (3.0%).

CONCLUSIONS

This is by far the largest routine clinical practice report of HPV-16/18 genotyping and histopathologic examination in negative-cytology women and the first report of such an investigation in the Chinese population. This study indicates enhanced risk stratification with HPV-16/18 genotype testing in HPV-positive, cytology-negative women in the Chinese population.

Carcinogenic risk of human papillomavirus (HPV) genotypes and potential effects of HPV vaccines in Korea

This study investigated the distribution of HPV types in Korean women and evaluated the carcinogenic risk of individual HPV types and the potential effects of HPV vaccines. A total of 4,081 HPV-positive samples between 2014 and 2017 were included. The most prevalent genotypes were HPV 16, 58, 68, and 56. Among them, HPV 16 was significantly higher in high-grade squamous intraepithelial neoplasia or worse (HSIL+ ) group. In cytologically evaluating the risk for HSIL+ by individual HPV types, HPV 16 was associated with the highest risk of HSIL+ (OR = 10.82; 95% CI: 7.93–14.77), followed by HPV 33, 31, 52, 18, 58, 51, and 35, in descending order (OR = 3.50 [type 33] to 2.62 [type 35]). Among those types, HPV 16, 18, 31, 33, and 58 were also significantly associated with HSIL+ on histologic evaluation. The analysis of the HPV subgroups covered by the different vaccines revealed that the HPV types covered by the 9-valent vaccine had a high association with HSIL+ (OR = 4.09; 95% CI: 3.02–5.54). Our findings highlight the different carcinogenic risks posed by the high risk HPV genotypes and the positive potential effects of the 9-valent HPV vaccine in reducing HPV-associated cervical cancer in Korea.

Comparison of clinical performance of two high-throughput liquid bead microarray assays, GeneFinder and CareGENE, for cervical screening in the general population

Recently, a clinical need for an improved human papilloma virus (HPV) test that covers a broad range of genotypes has emerged as a valuable primary screening tool for cervical lesions. The liquid bead microarray (LBMA) assay is a recently developed high-throughput platform covering a broad range of genotypes. Here, we compared the clinical performance of two recently developed LBMA assays, GeneFinder^TM HPV Liquid Bead Microarray (GeneFinder) and CareGENE^TM HPV genotyping kit-O (CareGENE), in the Korean general population. A total of 3,148 cervical swabs were tested by the GeneFinder and CareGENE assays. Cases with discrepant results between the two assays were subjected to direct sequencing as a reference method for evaluating the performance of the two LBMA assays. Among all swabs tested, 12.6% showed HPV positivity, and the prevalent HPV genotypes were HPV53, 70, 16, 39, and 51, in that order. The concordance rates between the two assays for the detection of HPV and for genotyping were 96.6% (kappa = 0.836) and 94.5% (kappa = 0.779), respectively. The two LBMA assays showed comparable sensitivity and specificity for HPV detection (GeneFinder: sensitivity 94.4% and specificity 98.7%, CareGENE: sensitivity 89.8% and specificity 99.6%) and for genotyping (GeneFinder: sensitivity 91.0% and specificity 96.6%, CareGENE: sensitivity 90.2% and specificity 99.1%). This is the first demonstration that CareGENE has comparable clinical performance to GeneFinder, which has been established to show excellent performance for screening HPV in previous studies. Both LBMA platforms are thus considered to be valuable tools for HPV detection and genotyping to improve cervical screening in the general population.

Screening for HPV infection in exfoliated cervical cells of women from different ethnic groups in Yili, Xinjiang, China

We investigated the infection status and genotype distribution of human papillomavirus (HPV) in women of different ages and various ethnic groups in the Yili region, Xinjiang, China. We checked the HPV genotypes of 3,445 samples of exfoliated cervical cells using the PCR–reverse dot blot method. The total infection rate of HPV was 25.60% (882/3,445). The ethnic stratification showed that the infection rates were 22.87% (196/857) in Uygur, 21.55% (122/566) in Kazak, and 27.89% (564/2,022) in Han individuals. The most prevalent high-risk genotypes were HPV16, HPV52, and HPV53 in Uygur and Kazak and HPV16, HPV52, and HPV58 in Han ethnic groups. The age stratification showed that the infection rates in Han, Uygur, and Kazak women were up to 40.9% (61/149) in those aged 26–30 years, 41.5% (22/53) in those over 61 years old, and 30.2% (29/96) in those 46–50 years old, respectively. Therefore, HPV infection and HPV genotype distribution varied among the different age groups of the three ethnic groups.

Clinical validation of the PCR-reverse dot blot human papillomavirus genotyping test in cervical lesions from Chinese women in the Fujian province: a hospital-based population study

Objective

To determine the clinical significance of the polymerase chain reaction (PCR)-reverse dot blot (RDB) human papillomavirus (HPV) genotyping assay in cervical cancer screening.

Methods

A total of 10,442 women attending the Fujian Provincial Maternity and Children's Health Hospital were evaluated using the liquid-based cytology (thinprep cytologic test [TCT]) and the PCR-RDB HPV test. Women with HPV infection and/or abnormal cytology were referred for colposcopy and biopsy. For HPV DNA sequencing, 120 specimens were randomly selected. Pathological diagnosis was used as the gold standard.

Results

Using the PCR-RDB HPV test, overall HPV prevalence was 20.57% (2,148/10,442) and that of high-risk (HR)-HPV infection was 18.68% (1,951/10,442). There was 99.2% concordance between HPV PCR-RDB testing and sequencing. In this studied population, the most common HR-HPV types were HPV-16, -52, -58, -18, -53, -33, and -51, rank from high to low. HPV-16, -18, -58, -59, and -33 were the top 5 prevalent genotypes in cervical cancer but HPV-16, -18, -59, -45, and -33 were the top 5 highest risk factors for cancer (odds ratio [OR]=34.964, 7.278, 6.728, 6.101, and 3.658; all p<0.05, respectively). Among 10,442 cases, 1,278 had abnormal cytology results, of which, the HR-HPV positivity rate was 83.02% (1,061/1,278). To screen for cervical cancer by PCR-RDB HPV testing, when using CIN2+, CIN3+, and cancer as observed endpoints, the sensitivity was 90.43%, 92.61%, and 94.78% and the negative predictive value (NPV) was 99.06%, 99.42%, and 99.78%, respectively. PCR-RDB HPV and TCT co-testing achieved the highest sensitivity and NPV.

Conclusion

For cervical cancer screening, the PCR-RDB HPV test can provide a reliable and sensitive clinical reference.

Can human papillomavirus (HPV) genotyping classify non-16/18 high-risk HPV infection by risk stratification?

Objective

Infection with high-risk genotypes of human papillomavirus (HR-HPV) is the major cause of invasive cervical cancers. HPV-16 and HPV-18 are known to be responsible for two-thirds of all invasive cervical carcinomas, followed by HPV-45, -31, and -33. Current guidelines only differentiate HPV-16/18 (+) by recommending direct colposcopy for treatment. We tried to evaluate whether there are differences in risk among 12 non-16/18 HR-HPV genotypes in this study.

Methods

The pathology archive database records of 1,102 consecutive gynecologic patients, who had results for cervical cytology and histology and for HPV testing, as determined by HPV 9G DNA chip, were reviewed.

Results

Among the 1,102 patients, 346 were non-16/18 HR-HPV (+) and 231 were HPV-16/18 (+). We calculated the odds ratios for ≥cervical intraepithelial neoplasia 2 (CIN 2) of 14 groups of each HR-HPV genotype compared with a group of HR-HPV (–) patients. Based on the odds ratio of each genotype, we divided patients with non-16/18 HR-HPV genotypes (+) into two groups: HPV-31/33/35/45/52/58 (+) and HPV-39/51/56/59/66/68 (+). The age-adjusted odds ratios for ≥CIN 2 of the HPV-31/33/35/45/52/58 (+) and HPV-39/51/56/59/66/68 (+) groups compared with a HR-HPV (–) group were 11.9 (95% CI, 7.6 to 18.8; p<0.001) and 2.4 (95% CI, 1.4 to 4.3; p<0.001), respectively, while that of the HPV-16/18 (+) group was 18.1 (95% CI, 11.6 to 28.3; p=0.003).

Conclusion

The 12 non-16/18 HR-HPV genotypes can be further categorized (HPV-31/33/35/45/52/58 vs. HPV-39/51/56/59/66/68) by risk stratification. The HPV-31/33/35/45/52/58 genotypes might need more aggressive action. Large scale clinical trials or cohort studies are necessary to confirm our suggestion.