Nonisotopic detection of human papillomavirus DNA in clinical specimens using a consensus PCR and a generic probe mix in an enzyme-linked immunosorbent assay format

Molecular detection methods of human papillomavirus (HPV)

Human papillomavirus (HPV) testing can identify women at risk of cervical cancer. Currently, molecular detection methods are the gold standard for identification of HPV. The three categories of molecular assays that are available are based on the detection of HPV DNA and include (1) non-amplified hybridization assays, such as Southern transfer hybridization (STH), dot blot hybridization (DB) and in situ hybridization (ISH); (2) signal amplified hybridization assays, such as hybrid capture assays (HC2); (3) target amplification assays, such as polymerase chain reaction (PCR) and in situ PCR. STH requires large amounts of DNA, is laborious and not reproducible, while ISH has only moderate sensitivity for HPV. The sensitivity of the HC2 assay is similar to that of PCR-based assays, with high sensitivity being achieved by signal rather than target amplification. PCR-based detection is both highly sensitive and specific. Since PCR can be performed on very small amounts of DNA, it is ideal for use on specimens with low DNA content. In the future, with the advance of technology, viral DNA extraction and amplification systems will become more rapid, more sensitive, and more automated.

Generic microtiter plate assay for triaging clinical specimens prior to genotyping of human papillomavirus DNA via consensus PCR

A generic human papillomavirus (HPV) probe assay was compared to the Linear Array to detect HPV DNA in 1,013 clinical specimens. The sensitivity, specificity, and negative predictive value of the assay were 99.5% (95% confidence interval [CI], 98.4% to 99.9%), 58.6% (95% CI, 53.9% to 63.1%), and 98.9% (95% CI, 96.5% to 99.8%), respectively. This assay conveniently identifies HPV-positive specimens.

Correlates of human papillomavirus viral load with infection site in asymptomatic men

Numerous studies have evaluated human papillomavirus (HPV) DNA load in women, especially HPV-16 viral load, and its role in cervical carcinogenicity. Few studies have examined HPV viral load in men, none among asymptomatic men. The aim of the current study is to quantify HPV-16 viral load in male anogenital specimens and to explore its correlates with anatomic sites. Two-hundred and ninety-four specimens from 42 men who tested positive for HPV-16 at one or more anatomic sites were evaluated. HPV DNA was detected with PGMY 09/11 primer and genotyped with reverse line blot assay followed by HPV-16 viral quantification using type-specific real-time PCR assay (TaqMan). The quantitative PCR assay showed a higher sensitivity in HPV-16 viral DNA detection compared with the reverse line blot assay. Viral load varied significantly by anatomic site (P = 0.019). Penile shaft specimens had significantly higher viral load than any other anatomic site evaluated except for the anal canal. HPV-16 viral load was positively correlated between proximal anatomic sites: perianal and anal canal (P = 0.003), perianal and scrotum (P = 0.011), scrotum and glans/corona (P = 0.045), and scrotum and penile shaft (P = 0.037). In conclusion, the penile shaft seemed to be the preferred site for HPV-16 viral replication. Viral load correlation between proximal sites suggested a possible autoinoculation in male HPV transmission.

Evaluation of the SPF10-INNO LiPA human papillomavirus (HPV) genotyping test and the roche linear array HPV genotyping test

The need for accurate genotyping of human papillomavirus (HPV) infections is becoming increasingly important, since (i) the oncogenic potential among the high-risk HPV genotypes varies in the pathogenesis of cervical cancer, (ii) monitoring multivalent HPV vaccines is essential to investigate the efficiency of the vaccines, and (iii) genotyping is crucial in epidemiologic studies evaluating HPV infections worldwide. Various genotyping assays have been developed to meet this demand. Comparison of different studies that use various HPV genotyping tests is possible only after a performance assessment of the different assays. In the present study, the SPF(10) LiPA version 1 and the recently launched Roche Linear Array HPV genotyping assays are compared. A total of 573 liquid-based cytology samples were tested for the presence of HPV by a DNA enzyme immunoassay; 210 were found to be positive for HPV DNA and were evaluated using both genotyping assays (163 with normal cytology, 22 with atypical squamous cells of undetermined significance, 20 with mild/moderate dysplasia, and 5 with severe dysplasia). Comparison analysis was limited to the HPV genotype probes common to both assays. Of the 160 samples used for comparison analysis, 129 (80.6%) showed absolute agreement between the assays (concordant), 18 (11.2%) showed correspondence for some but not all genotypes detected on both strips (compatible), and the remaining 13 (8.2%) samples did not show any similarity between the tests (discordant). The overall intertest comparison agreement for all individually detectable genotypes was considered very good (kappa value, 0.79). The genotyping assays were therefore highly comparable and reproducible.

Enhanced detection and typing of human papillomavirus (HPV) DNA in anogenital samples with PGMY primers and the Linear array HPV genotyping test

The Roche PGMY primer-based research prototype line blot assay (PGMY-LB) is a convenient tool in epidemiological studies for the detection and typing of human papillomavirus (HPV) DNA. This assay has been optimized and is being commercialized as the Linear Array HPV genotyping test (LA-HPV). We assessed the agreement between LA-HPV and PGMY-LB for detection and typing of 37 HPV genotypes in 528 anogenital samples (236 anal, 146 physician-collected cervical, and 146 self-collected cervicovaginal swabs) obtained from human immunodeficiency virus-seropositive individuals (236 men and 146 women). HPV DNA was detected in 433 (82.0%) and 458 (86.7%) samples with PGMY-LB and LA-HPV (P = 0.047), respectively, for an excellent agreement of 93.8% (kappa = 0.76). Of the 17,094 HPV typing results, 16,562 (1,743 positive and 14,819 negative results) were concordant between tests (agreement = 96.9%; kappa = 0.76). The mean agreement between tests for each type was 96.4% +/- 2.4% (95% confidence interval [CI], 95.6% to 97.2%; range, 86% to 100%), for an excellent mean kappa value of 0.85 +/- 0.10 (95% CI, 0.82 to 0.87). However, detection rates for most HPV types were greater with LA-HPV. The mean number of types per sample detected by LA-HPV (4.2 +/- 3.4; 95% CI, 3.9 to 4.5; median, 3.0) was greater than that for PGMY-LB (3.4 +/- 3.0; 95% CI, 3.1 to 3.6; median, 2.0) (P < 0.001). The number of types detected in excess by LA-HPV in anal samples correlated with the number of types per sample (r = 0.49 +/- 0.06; P = 0.001) but not with patient age (r = 0.03 +/- 0.06; P = 0.57), CD4 cell counts (r = 0.06 +/- 0.06; P = 0.13), or the grade of anal disease (r = -0.11 +/- 0.06; P = 0.07). LA-HPV compared favorably with PGMY-LB but yielded higher detection rates for newer and well-known HPV types.

Molecular diagnosis of human papillomavirus (HPV) infections

Human papillomaviruses (HPVs) comprise more than 100 genotypes. The mucosal types can be divided into high-risk and low-risk (LR) types depending on the associated disease risk. HPV infection is mainly diagnosed by molecular methods, since reliable serological tools are not available and culture of the virus is not possible. Accurate molecular diagnostic techniques that can be used to inform patient management and follow-up after treatment are now available for detection and identification of HPV. The diagnosis of HPV infections in patients at risk of disease in a clinical setting requires a different approach from that used for epidemiological studies, vaccination trials and natural history studies. This review describes the different molecular methods available for HPV detection and genotyping and their possible clinical utility.

Facile, comprehensive, high-throughput genotyping of human genital papillomaviruses using spectrally addressable liquid bead microarrays

Human papillomavirus (HPV) is the worldwide cause of carcinoma of the uterine cervix, a cancer that is the second most common neoplasm in women, resulting in nearly 250,000 deaths a year. The magnitude of the risk of cancer after HPV infection, however, is virus type-specific. Over 40 HPV types can infect the genital tract. Comprehensive, high-throughput typing assays for HPV, however, are not currently available. Blending multiplex PCR and multiplex hybridization using spectrally addressable liquid bead microarrays we have developed a high-throughput, fast, single-tube-typing assay capable of simultaneously typing 45 HPV. The overall incidence of HPV in 429 women tested using this new assay was 72.2% for those with squamous intraepithelial lesions, 51.5% for those with atypical squamous cells of undetermined significance and 15.4% for women with normal cytology, respectively. This compared well with the incidence of HPV detected by a parallel non-typing generic high-risk assay. The new assay detected a wide spectrum of HPV types and a high incidence of mixed infections. We believe our assay may find widespread applications in areas requiring virus type-specific information, such as in epidemiological studies, cancer screening programs, monitoring therapeutic interventions, and evaluating the efficacy of HPV vaccine trials.

Human papillomavirus testing for primary screening in women at low risk of developing cervical cancer. The Greek experience

OBJECTIVE

To compare the performance of human papillomavirus (HPV) DNA detection against routine Papanicolaou smear for the detection of low- and high-grade cervical intraepithelial neoplasia in a low-risk population.

MATERIALS AND METHODS

A cross-sectional study was performed involving 1296 women attending six outpatient clinics in Northern Greece (Thessaloniki, Thermi, Mihaniona, Corfu, Veria, and Serres). Women underwent a gynecological examination, including collection of exfoliated cervical cells for Papanicolaou cytology and HPV DNA detection. Cytology was processed according the conventional routine manner, and HPV DNA was determined using the polymerase chain reaction technique. In positive cases of either method, a complete colposcopic evaluation was performed with directed biopsies. Tests (HPV DNA, cytology, and colposcopy) performance characteristics were determined using the histopathologic diagnosis as the reference standard.

RESULTS

HPV DNA testing showed a significantly better sensitivity than the Papanicolaou smear in detecting cervical intraepithelial neoplasia (75% versus 50% for high-grade lesions and 81.2% versus 50% for lesions of any grade, respectively). Specificity, and positive and negative predictive values did not significantly differ. Even after dividing women in younger or older than 30 years, the sensitivity of the HPV DNA test was greater than cytology (100% and 70% versus 50% for cytology in both groups, respectively), with a 6.3% loss in specificity when performed in women younger than 30 years.

CONCLUSION

HPV testing could be useful in screening women at low risk for cervical cancer, either as an adjunct tool to augment existing cytology programs or as a unique test of its own.

Cervical human papillomavirus infection in women attending gynaecological outpatient clinics in northern Greece

Human papillomavirus (HPV) is the necessary cause for the development of invasive cervical cancer. Identification of HPV determinants may contribute to the targeting of high-risk groups for cervical cancer. The study was aimed at estimating HPV prevalence and its determinants among 1296 women attending six gynaecological outpatient clinics in northern Greece. Information was available through personal interview and the study of cervical exfoliated cells. HPV DNA was detected by reverse line-blot polymerase chain reaction using the L1 primers PGMY09/11. The overall HPV prevalence was 2.5%. After controlling for potential confounders, the two independent risk factors associated with an increased prevalence were young age and parity. The prevalence odds ratio (POR) for those younger than 27 years against those older than 42 years was 5.31 (95% confidence interval (CI)=1.53-18.44) and the POR for nulliparous women compared with women with two or more children was 4.15 (95% CI=1.35-12.76). HPV was present in 10 of 12 women with low-grade cervical intraepithelial lesions (CIN) (83.3%) and in 3 of 4 with high-grade CIN (75%). The prevalence of genital HPV infections in the study population was among the lowest ever reported internationally.

Detection of human papillomavirus DNA in cervical samples: analysis of the new PGMY-PCR compared to the hybrid capture II and MY-PCR assays and a two-step nested PCR assay

The PGMY-PCR for human papillomavirus (HPV) was evaluated, in parallel with nested PCR (nPCR), in samples with noted Hybrid Capture II (HCII) and MY-PCR results. PGMY-PCR detected HPV DNA in 2.5% of HCII-negative-MY-PCR-negative samples and in 71.7% of HCII-positive-MY-PCR-negative samples; also, it detected the MY-PCR-negative-nPCR-negative types HPV-42, HPV-44, HPV-51, HPV-87, and HPV-89.

Chapter 12: Human papillomavirus technologies

Currently, human papillomavirus (HPV) DNA tests validated in large trials and epidemiological studies are the hybrid capture second-generation (HC2) HPV DNA assay and a variety of polymerase chain reaction (PCR) protocols employing degenerate or consensus primers. This article describes the currently available technology for HPV detection and discusses novel technologies and their potential for large-scale screening. Ideally, an HPV test should allow detection of multiple HPV types, identify individual types, and provide quantitative information about the viral load of each individual type found. Moreover, it should be easy to perform, be highly reproducible, with a high specificity and sensitivity, and amenable for high throughput analysis and automation. Because we do not yet fully understand the true value of viral load and the biological relevance of the different HPV types, any HPV test should be able to detect the clinically relevant high-risk types with a sufficient sensitivity of at least 10 000 genome copies per sample. To validate the different current and future test systems and to compare inter-laboratory performance we urgently need reference samples, validated reagents, and standardized protocols.

Inclusion of HPV testing in routine cervical cancer screening for women above 29 years in Germany: results for 8466 patients

In a prospective cohort study 8466 women attending routine cervical cancer screening were recruited. Colposcopy was performed on women with any degree of atypia on cytology and/or a positive high-risk human papillomavirus (HPV)-DNA test (HC2; Hybrid Capture 2((c))), and for a randomly selected sample of 3.4% women with negative findings on both. Quality control included reviews of cytology, histology, colposcopy images and retesting of samples with polymerase chain reaction. Test diagnostic performances were based on 7908 women who had complete baseline and follow-up results. Routine histology identified 86 women with high-grade cervical intraepithelial neoplasia (CIN2+), which was confirmed by review histology in only 46 cases. Sensitivity of routine cytology for the detection of CIN2+ was 43.5%, with a specificity, positive predictive value (PPV), negative predictive value (NPV) of 98.0, 11.4 and 99.7%, respectively. Sensitivity of the HC2 test for the detection of CIN2+ was 97.8%, with a specificity, PPV and NPV, of 95.3, 10.9 and 100%, respectively. No high-grade neoplasia was detected in the randomly selected control group. A negative HPV-test result, even in combination with a positive Papanicolaou (Pap) result, virtually excluded any risk of underlying high-grade disease, but this was not the case for a negative Pap result. These data show that HPV testing is of value for the detection or exclusion of prevalent CIN in a routine cervical cancer-screening setting and could be used for further risk classification of women for follow-up management.

International proficiency study of a consensus L1 PCR assay for the detection and typing of human papillomavirus DNA: evaluation of accuracy and intralaboratory and interlaboratory agreement

The PGMY L1 consensus primer pair combined with the line blot assay allows the detection of 27 genital human papillomavirus (HPV) genotypes. We conducted an intralaboratory and interlaboratory agreement study to assess the accuracy and reproducibility of PCR for HPV DNA detection and typing using the PGMY primers and typing amplicons with the line blot (PGMY-LB) assay. A test panel of 109 samples consisting of 29 HPV-negative (10 buffer controls and 19 genital samples) and 80 HPV-positive samples (60 genital samples and 20 controls with small or large amounts of HPV DNA plasmids) were tested blindly in triplicate by three laboratories. Intralaboratory agreement ranged from 86 to 98% for HPV DNA detection. PGMY-LB assay results for samples with a low copy number of HPV DNA were less reproducible. The rate of intralaboratory agreement excluding negative results for HPV typing ranged from 78 to 96%. Interlaboratory reliability for HPV DNA positivity and HPV typing was very good, with levels of agreement of >95% and kappa values of >0.87. Again, low-copy-number samples were more prone to generating discrepant results. The accuracy varied from 91 to 100% for HPV DNA positivity and from 90 to 100% for HPV typing. HPV testing can thus be accomplished reliably with PCR by using a standardized written protocol and quality-controlled reagents. The use of validated HPV DNA detection and typing assays demonstrating excellent interlaboratory agreement will allow investigators to better compare results between epidemiological studies.

Comparisons of HPV DNA detection by MY09/11 PCR methods

Two modifications to the original L1 consensus primer human papillomavirus (HPV) PCR method, MY09-MY011, using AmpliTaq DNA polymerase (MY-Taq), were evaluated for HPV DNA detection on clinical specimens from a cohort study of cervical cancer in Costa Rica. First, HPV DNA testing of 2978 clinical specimens by MY09-MY011 primer set, using AmpliTaq Gold DNA polymerase (MY-Gold) were compared with MY-Taq testing. There was 86.8% total agreement (kappa = 0.72, 95%CI = 0.70-75) and 69.6% agreement among positives between MY-Gold and MY-Taq. MY-Gold detected 38% more HPV infections (P < 0.0001) and 45% more cancer-associated (high-risk) HPV types (P < 0.0001) than MY-Taq, including 12 of the 13 high-risk HPV types. Analyses of discordant results using cytologic diagnoses and detection of HPV DNA by the Hybrid Capture 2 Test suggested that MY-Gold preferentially detected DNA positive specimens with lower HPV viral loads compared with MY-Taq. In a separate analysis, PGMY09-PGMY11 (PGMY-Gold), a redesigned MY09/11 primer set, was compared with MY-Gold for HPV DNA detection (n = 439). There was very good agreement between the two methods (kappa = 0.83; 95%CI = 0.77-0.88) and surprisingly no significant differences in HPV detection (P = 0.41). In conclusion, we found MY-Gold to be a more sensitive assay for the detection of HPV DNA than MY-Taq. Our data also suggest that studies reporting HPV DNA detection by PCR need to report the type of polymerase used, as well as other assay specifics, and underscore the need for worldwide standards of testing.

Molecular detection and genotyping of human papillomavirus

Human papillomavirus infections are associated with the development of cervical neoplasia. Human papillomavirus is a group of heterogeneous viruses, comprising many genotypes, which can be divided into high-risk and low-risk types, depending on their association with disease. Therefore, accurate molecular diagnostic tools are required for detection and identification of human papillomavirus. Monitoring of human papillomavirus infection is necessary for adequate patient management and follow-up during treatment. This review describes the different molecular methods available for human papillomavirus detection and identification of genotypes.

Current methods of testing for human papillomavirus

Human papillomavirus DNA testing is gaining wider acceptance, yet the majority of testing is still undertaken in the research setting using protocols that are unsuitable for clinical diagnostic laboratories. Large-scale clinical human papillomavirus DNA testing is likely to be introduced as an adjunct to cervical cytology, so the cytology laboratory is an appropriate place for it to be undertaken. This poses a challenge for any human papillomavirus DNA test since it will be performed by technicians not specifically trained in virology or molecular biology, and will need to produce consistently reliable results in this setting. This is only realistically possible with a standardized and quality-controlled, commercially produced human papillomavirus DNA test. There is currently only one such commercially available assay, although there are a number of research-based tests that could logically lead to additional commercial products. The technological basis of these assays, together with available performance data, is reviewed in this chapter and the clinical utility of the tests is evaluated.