Comparison of dot filter hybridization, Southern transfer hybridization, and polymerase chain reaction amplification for diagnosis of anal human papillomavirus infection

Effect of Human Immunodeficiency Virus Infection on Human Papillomavirus Clearance Among Women in Senegal, West Africa

BACKGROUND

Persistent infection with high-risk human papillomavirus (HPV) is associated with development of invasive cervical cancer.

METHODS

Longitudinal data was collected from 174 Senegalese women. We employed marginal Cox proportional hazards models to examine the effect of human immunodeficiency virus (HIV) status (HIV positive vs HIV negative) and HIV type (HIV-1 vs HIV-2 vs dual HIV-1/HIV-2) on clearance of type-specific HPV infection. Analyses were stratified by incident versus prevalent HPV infection.

RESULTS

Incident HPV infections in HIV-positive women were less likely to clear than those in HIV-negative women (adjusted hazard ratio [HR] = 0.60; 95% confidence interval [CI], .38-.94). Among HIV-positive women, HIV-2-infected women and HIV-1/2 dually infected women were more likely to clear HPV incident infections than HIV-1-infected women (HR = 1.66; 95% CI, .95-2.92 and HR = 2.17; 95% CI, 1.12-4.22, respectively). Incident HPV infections in HIV-positive women with CD4 cell count ≤500 cells/μL were less likely to clear than those in HIV-positive women with CD4 cell count >500 cells/μL (HR = 0.65; 95% CI, .42-1.01). No significant associations were observed for prevalent HPV infections.

CONCLUSIONS

HIV infection reduced the likelihood of clearance of incident HPV infection. Furthermore, among HIV-positive women, low CD4 cell count and dual HIV infection were each associated with reduced likelihood of clearance.

A Comparison of the Natural History of HPV Infection and Cervical Abnormalities among HIV-Positive and HIV-Negative Women in Senegal, Africa

Background: There is evidence of an interaction between HIV and human papillomavirus (HPV) resulting in increased HPV-associated morbidity and cancer mortality among HIV-positive women. This study aims to determine how the natural history of cervical HPV infection differs by HIV status.Methods: A total of 1,320 women (47% were positive for HIV-1 and/or HIV-2) were followed for an average of two years in Senegal, West Africa between 1994 and 2010. Cytology (with a sub-sample of histology) and HPV DNA testing were performed at approximately 4-month intervals yielding data from over 7,900 clinic visits. Competing risk modeling was used to estimate rates for transitioning between three clinically relevant natural history stages: Normal, HPV, and HSIL (high-grade squamous intraepithelial lesions). Among HIV-positive women, exploratory univariate analyses were conducted examining the impact of HPV type, infection with multiple HPV types, HIV type, CD4⁺ count, and age.Results: HIV-positive women had higher rates of progression and lower rates of regression compared with HIV-negative women (i.e., adverse transitions). HIV-positive women had a 2.55 [95% confidence interval (CI), 1.69-3.86; P < 0.0001] times higher rate of progression from HPV to HSIL than HIV-negative women (with 24-month absolute risks of 0.18 and 0.07, respectively). Among HIV-positive women, HPV-16/18 infection and CD4⁺ count <200/mm³ were associated with adverse transitions.Conclusions: Adverse HIV effects persist throughout HPV natural history stages.Impact: In the limited-resource setting of sub-Saharan Africa where cervical cancer screening is not widely available, the high-risk population of HIV-positive women may be ideal for targeted screening. Cancer Epidemiol Biomarkers Prev; 26(6); 886-94. ©2017 AACR.

Human papillomavirus type 16 viral load in relation to HIV infection, cervical neoplasia and cancer in Senegal

BACKGROUND

The importance of human papillomavirus (HPV) viral load in the pathogenesis of cervical cancer among HIV-infected and HIV-uninfected women has not yet been established.

METHODS

In this cross-sectional study, HPV-16 viral loads were measured using previously-collected and frozen cervical swab samples from 498 HPV-16 positive Senegalese women (368 HIV-seronegative, 126 HIV-1 and/or HIV-2 seropositive). The real-time polymerase chain reaction assay was used to quantify HPV-16 E7 copy number normalized by human cellular DNA (β-actin), and viral loads were log10 transformed. Associations between HPV-16 viral load, degree of cervical abnormality, and HIV status were assessed using multinomial and linear regression methods.

RESULTS

Compared to women with normal cytology, the likelihood of CIN1 (ORa: 1.21, 95% CI 0.93-1.57), CIN2-3 (ORa: 2.38, 95% CI 1.72-3.29) and cancer (ORa: 2.12, 95% CI 1.52-2.96) was found to increase for each 1-unit log10 increase in HPV-16 viral load. Compared to HIV-negative women, HIV-positive women had higher average HPV-16 viral load values (βa: 0.39, 95% CI 0.03-0.75), even after accounting for degree of cervical abnormality.

CONCLUSION

In our study of women including those with cancer, HPV-16 viral load was associated with a higher likelihood of cervical abnormalities. However, substantial overlaps across categories of disease severity existed. Higher viral load among HIV-infected individuals may indicate that HIV infection influences HPV viral replication factors.

Influence of HIV-1 and/or HIV-2 infection and CD4 count on cervical HPV DNA detection in women from Senegal, West Africa

BACKGROUND

HIV infection is associated with greater risk of precancerous lesions and cervical cancer in women. However, several factors remain unclarified regarding the association between HIV infection and HPV detection, especially among those with HIV type 2 versus type 1 infection and severely immunocompromised persons.

OBJECTIVES

To evaluate HPV overall and type-specific detection among HIV-infected and uninfected women in Senegal.

STUDY DESIGN

Detection of HPV DNA for 38 genotypes in cervical swabs using PCR-based methods was evaluated in HIV-positive (n=467) and HIV-negative (n=2139) women participating in studies in Senegal. Among HIV-1 and/or HIV-2 positive women, CD4 counts were assessed. Adjusted multivariable prevalence ratios (PR) were calculated.

RESULTS

The prevalence of any HPV DNA and multiple HPV types was greater among HIV-infected individuals (78.2% and 62.3%, respectively) compared with HIV-negative women (27.1% and 11.6%). This trend was also seen for HPV types 16 and 18 (13.1% and 10.9%) compared to HIV-negative women (2.2% and 1.7%). HIV-infected women with CD4 cell counts less than 200 cells/μl had a higher likelihood of any HPV detection (PRa 1.30; 95% CI 1.07-1.59), multiple HPV types (PRa 1.52; 95% CI 1.14-2.01), and HPV-16 (PRa 9.00; 95% CI 1.66-48.67), but not HPV-18 (PRa 1.20, 95% CI 0.45-3.24) compared to those with CD4 counts 500 cells/μl or above.

CONCLUSION

HIV-infected women, especially those most severely immunocompromised, are more likely to harbor HPV. Measures to prevent initial HPV infection and subsequent development of cervical cancer through focused screening efforts should be implemented in these high risk populations.

Epidemiology of HPV in HIV-positive and HIV-negative fertile women in Cameroon, West Africa

BACKGROUND

HPV types vary by country and HIV status. There are no data on the prevalent HPV genotypes from Cameroon.

METHODS

We conducted a cross-sectional, observational study on 65 Cameroonian women. Samples were sent for HPV genotyping and Thin Prep analyses.

RESULTS

41 out of 61 samples tested (67.2%) had HPV subtypes detected. The most common high risk types encountered were: 45 (24.6%) and 58 (21.5%). HIV-positive women were more likely to test positive for any HPV (P = .014), have more than one HPV subtype (P = .003), and to test positive for the high risk subtypes (P = .007). Of those with high risk HPV, HIV-positive women were more likely to have Thin Prep abnormalities than HIV-negative women (P = .013).

CONCLUSIONS

Oncogenic HPV subtypes 45 and 58 were more prevalent than those subtypes carried in the quadrivalent vaccine. Further studies are needed to assess whether the current vaccine will be effective in this region.

Prevalence of sexually transmissible pathogens in semen from asymptomatic male infertility patients with and without leukocytospermia

OBJECTIVE

To determine the prevalence of pathogens that cause sexually transmitted infections (STIs) in semen from asymptomatic male infertility patients with and without leukocytospermia (LCS), and associations between STIs, inflammatory markers, and other semen variables.

DESIGN

Retrospective, controlled study.

SETTING

Academic Medical Center.

PATIENT(S)

Two hundred and forty-one male infertility patients undergoing routine semen analysis: 132 with LCS, and 109 without LCS.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

The DNA from STI pathogens (human papillomavirus [HPV], cytomegalovirus [CMV], herpes simplex virus [HSV], human herpesvirus type 6 [HHV-6], Epstein-Barr virus [EBV], hepatitis B virus [HBV], and Chlamydia trachomatis [CT]), routine semen parameters, and markers of accessory gland and epididymal function and inflammation.

RESULT(S)

The DNA from STI pathogens was detected in 45/241 (18.7%) of the samples (CMV, 8.7%; HPV, 4.5%; HHV-6, 3.7%; HSV, 3.7%; CT, 2.5%; EBV, 0.4%; and HBV, 0%), with no difference in prevalence between the LCS and non-LCS groups. The DNA of STI pathogens in semen was associated with a decrease in sperm concentration, motile sperm concentration, total sperm count, and neutral alpha-glucosidase concentration, whereas LCS was associated with a decrease in total sperm count, percent normal forms, and fructose concentration.

CONCLUSION(S)

The DNA of STI pathogens was detected in semen from a high percentage of asymptomatic male infertility patients, and was associated with poor semen quality. Efforts to diagnose and treat subclinical genital-tract infections should be intensified.

Incident High-Grade Squamous Intraepithelial Lesions in Senegalese Women With and Without Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2

BACKGROUND

Women infected with human immunodeficiency virus type 1 (HIV-1) and -2 may be at higher risk of developing cervical cancer than uninfected women. We assessed the relationships among human papillomavirus (HPV) types and persistence, HIV-1 and/or HIV-2 infection, and the development of high-grade cervical squamous intraepithelial lesions (HSILs) in a prospective study.

METHODS

We studied 627 women with and without HIV-1 and/or HIV-2 infection and high-risk HPV infection in Senegal, West Africa, who were assessed every 4 months for HSIL and HPV DNA over a mean follow-up of 2.2 years. Cox regression modeling was used to assess risks associated with development of HSIL.

RESULTS

During follow-up, 71 (11%) of 627 women developed HSIL as detected by cytology. HIV-infected women with high-risk HPV types were at greatest risk for development of HSIL. In multivariable modeling, infection with oncogenic HPV types--both persistent (hazard ratio [HR] = 47.1, 95% confidence interval [CI] = 16.3 to 136) and transient (HR = 14.0, 95% CI = 3.7 to 54)--was strongly associated with HSIL risk. In univariate analyses, HIV-positive women infected with HIV-2 were less likely to develop HSIL (HR = 0.3, 95% CI = 0.1 to 0.9) than HIV-positive women infected with HIV-1. HIV-positive women with CD4+ cell counts between 200 and 500 cells per microliter (HR = 2.2, 95% CI = 0.8 to 6.3) or fewer than 200 cells per milliliter (HR = 5.5, 95% CI = 2.0 to 15.2) were at greater risk of HSIL than HIV-positive women with CD4 counts of more than 500 cells per milliliter. High plasma HIV RNA levels were associated with increased HSIL risk (HR for each order of magnitude increase in the level of plasma HIV RNA = 1.4, 95% CI = 1.1 to 1.7; P = .005). After adjustment for HPV types and persistence, however, HIV type, plasma HIV RNA level, and CD4 count were no longer statistically significantly associated with increased risk of HSIL.

CONCLUSIONS

HIV-1 and HIV-2 are associated with increased risk for development of HSIL. This risk appears to be associated primarily with increased HPV persistence that may result from immunosuppression related to HIV-1 and/or HIV-2 infection.

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.

Comparison of real-time PCR signal-amplified in situ hybridization and conventional PCR for detection and quantification of human papillomavirus in archival cervical cancer tissue

Archival paraffin-embedded tumor specimens offer a wealth of information for both cancer research and for routine clinical applications. However, the use of formalin-fixed, paraffin-embedded specimens for quantitative real-time PCR is not yet a standard diagnostic method in many laboratories, in particular for the quantification of human papillomavirus (HPV). Particularly high-risk HPV types are involved in almost 100% of the carcinogenesis of cervical cancer. We compared the diagnostic applicability and sensitivity of real-time PCR to that of chromogenic tyramide-signal-amplified in situ hybridization and conventional PCR for the detection of HPV from archival tissue in 164 cases of carcinoma in situ and cervical cancer. Furthermore, we examined whether the viral load of HPV is of prognostic relevance. Our findings indicate that patients in tumor stage I with a lower viral load of HPV type 16 (HPV16; up to 1,000 copies/ng of DNA) had a significantly better survival than HPV 16-negative patients (P = 0.037). We observed a greater sensitivity of both real-time PCR and conventional PCR for the detection of HPV16 and -18 compared to signal amplified in situ hybridization. We found a considerable concordance between HPV16 (kappa = 0.661) and HPV18 (kappa = 0.781) status as measured by real-time PCR and conventional PCR, indicating similar sensitivities. We recognized an inhibitory effect of formalin fixation and paraffin embedding on the evaluation of real-time PCR quantification.

Prevalence of specific types of human papillomavirus and cervical squamous intraepithelial lesions in consecutive, previously unscreened, West-African women over 35 years of age

Previous studies among women worldwide have demonstrated that infection with specific types of human papillomaviruses (HPV) is central to the pathogenesis of cervical neoplasia. There is little data, however, concerning the prevalence of specific HPV types and the association of each type with cervical neoplasia among women in sub-Saharan Africa, who remain at very high risk of cervical cancer. We studied 2,065 consecutive patients aged 35 years or older, presenting to community health clinics in Dakar and Pikine, West Africa, who had not been screened previously for cytologic abnormalities or HPV. Cytologic diagnosis and HPV detection were accomplished using a ThinPrep Pap and a polymerase chain reaction-based reverse-line strip assay, respectively. Odds ratios (OR) and associated 95% confidence intervals (CI) were estimated using polynomial logistic regression. Cytologic abnormalities were found in 426 women (20%), including 254 (12%) with atypical squamous cells of undetermined significance, 86 (4%) with low-grade squamous intraepithelial lesions, 66 (3%) with high-grade squamous intraepithelial lesions (HSIL) and 20 (1%) with invasive cancer. HPV infection was detected in 18%. Among women with negative cytologic findings, the prevalence of high risk but not low risk HPV types increased with age. HPV16 (2.4%) and HPV58 (1.6%) were the most frequently detected HPV types in this population, as well as being the most strongly associated with risk of HSIL/cancer (HPV16: OR = 88, 95% CI = 39-200; HPV58: OR = 51, 95% CI = 16-161). These data suggest that in addition to HPV16, HPV58 should be considered in the strategic planning of vaccination against cervical cancer in this geographic region.

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.

Detection and genotyping of human papillomavirus DNA by SPF10 and MY09/11 primers in cervical cells taken from women attending a colposcopy clinic

Human papillomavirus (HPV) is the main etiological agent of cervical cancer. There is a large number of HPV genotypes and therefore a need to distinguish the high risk HPV genotypes associated with invasive cancer from the low risk. Because persistence of high risk HPV infection is necessary for progression of a pre-invasive cervical change one needs to identify the individual genotype to see if it persists. PCR amplification of HPV DNA is described using two consensus primer systems from cervical cells. Amplified HPV DNA was genotyped using a reverse hybridization line probe assay (LiPA). HPV DNA was amplified from 42% of samples by MY09/11 and from 80% by SPF10. In 42 samples HPV DNA was detected by both primer sets and in 38 samples only the SPF10 primers detected HPV DNA. The LiPA detected 21 different HPV genotypes (13 high risk) in this cohort of samples. Forty-three percent contained a single HPV genotype and 24% contained multiple infections (2-5 genotypes). Overall, high risk HPV genotypes were detected in 48% of the cervical samples, the most frequent types were 16, 18, 31, and 51. The proportion of high risk HPV genotypes increased with more severe cytological abnormalities. This study demonstrates that the SPF10 primer set is more sensitive than the MY09/11 primer set and that genotyping by LiPA tells us if the HPV infection is caused by a high risk type and if the infection is mixed. Additionally LiPA provides information about the individual genotype when looking for persistence of infection. HPV DNA detection and genotyping is therefore a useful tool in the colposcopy clinic, used in conjunction with cytology.

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.

Intra-laboratory reproducibility of human papillomavirus identification in cervical specimens by a polymerase chain reaction-based assay

BACKGROUND

polymerase chain reaction (PCR)-based assays for human papillomavirus (HPV) sequences are in wide use in clinical and epidemiological studies. The reproducibility of these assays is not extensively studied.

OBJECTIVES

to estimate the intra-laboratory reproducibility of generic and type-specific HPV diagnoses by the MY09/MY11/HMB01 consensus L1 primer-based PCR assay.

STUDY DESIGN

systematically collected specimens (n=207) were masked and retested.

RESULTS

when specimens negative in both initial and repeat assays were excluded from analysis, the diagnostic reproducibility was 98. 6% for beta-globin, 90.7% for generic HPV (any HPV type), and 76.9% for type-specific HPVs. The reproducibility of type-specific diagnosis increased with increase in signal strength in the hybridization reaction of the initial assay. When a specimen contained five or more HPV types in the initial assay, it was rare to identify all of the HPV types in the repeat assay.

CONCLUSIONS

the degree of reproducibility of the PCR diagnosis should be taken into account in the interpretation of HPV data in clinical and epidemiological studies.

Mucosal swabs detect HPV in laryngeal papillomatosis patients but not family members

Seven patients, aged 2-7 years, with active recurrent respiratory papillomatosis (RRP) attending the University of Michigan Pediatric Otolaryngology Clinic were studied to determine if human papillomavirus (HPV) is harbored in sites of the upper aerodigestive tract other than in the laryngeal papilloma itself. We also determined if close family members had detectable virus in their oral cavities. Noninvasive swabs of buccal mucosa, posterior pharynx, nasal vestibule, and tonsillar pillar of patients, as well as buccal mucosa and posterior pharyngeal swabs of family members were studied. Swabs of the patients' papillomas served as the positive controls. HPV was detected using polymerase chain reaction (PCR) amplification and Southern hybridization techniques. Six of seven patients had detectable HPV in papilloma and endolaryngeal swabs. Four were HPV type 6, and two were HPV type 11. The patient whose swab was negative for HPV was found to be biopsy negative for papilloma 3 weeks after a single laser excision which was performed 6 months prior to the endolaryngeal swab. HPV types 16, 18 and 31 were not found in any of the patients. No swabs from other sites in patients or family members were HPV positive despite the presence of adequate DNA in the swabbed material for successful amplification of beta-actin sequences. The absence of HPV (other than in the papilloma itself) in the upper aerodigestive tract of patients and caregivers is consistent with the absence of reported cases of horizontal transmission to siblings or other family members. The findings are also consistent with the conventional view that juvenile respiratory HPV is transmitted vertically from vaginal condylomas in the mother.

Reliable high risk HPV DNA testing by polymerase chain reaction: an intermethod and intramethod comparison

BACKGROUND

The development of a reproducible, sensitive, and standardised human papillomavirus (HPV) polymerase chain reaction (PCR) test is required to implement HPV testing in cervical cancer screening programmes and for triaging women with mild to moderate dysplasia.

AIMS

To determine the intermethod agreement between different GP5+/6+ and MY09/11 PCR based protocols for the detection and typing of high risk (HR) HPV DNA in cervical smears and to assess the intramethod reproducibility of the GP5+/6+ PCR enzyme immunoassay (EIA) for HR-HPV detection.

METHODS

For the intermethod comparison, crude aliquots of 20 well characterised cervical smears comprising five HPV negative samples, and six and nine samples containing single and multiple HPV infections, respectively, were coded and sent from reference laboratory (A) to three other laboratories. One of these (laboratory B) used the GP5+/6+ PCR-EIA and was provided with standard protocols. Another laboratory (C) used GP5+/6+ PCR combined with sequence analysis and type specific PCR, whereas two laboratories (D and E) used MY09/11 PCR followed by restriction fragment length polymorphism (RFLP) analysis for the detection and typing of HR-HPV. The intramethod agreement of GP5+/6+ PCR-EIA was analysed in a subsequent study with four other laboratories (F to I) on crude aliquots of 50 well characterised cervical smears, consisting of 32 HR-HPV positive and 18 HPV negative samples. Standardised protocols, primers, and probes were also provided by the reference laboratory for HR-HPV detection.

RESULTS

In the intermethod comparison, pairwise agreement of the different laboratories with reference laboratory A for the detection of HR-HPV varied between 75% and 100% (kappa values: 0.5 to 1). Typing data revealed a broader range in pairwise agreement rates between 32% and 100%. The highest agreement was found between laboratories A and B using standardised protocols and validated reagents. In the intramethod evaluation, pairwise comparison of the laboratories F to I with reference laboratory A revealed excellent agreement rates from 92% to 100% (kappa values: 0.88 to 1.0) with an overall sensitivity of 97.5% (195/200) and specificity of 99.5% (199/200).

CONCLUSIONS

The detection of HR-HPV as a group is highly reproducible with GP5+/6+ PCR-EIA provided that standardised protocols and validated reagents are used.

High-risk human papillomavirus types and squamous cell carcinoma in patients with respiratory papillomas

Respiratory papillomas (RPs) are benign, virally induced tumors of the larynx and respiratory epithelium that may obstruct the airway and tend to recur frequently. RPs are thought to be the result of infection with the human papillomaviruses (HPVs) types 6 and 11. We surveyed archival RP specimens to determine whether there were correlations of HPV type with patient characteristics or clinical course. Paraffin-embedded papilloma specimens of 45 different patients were analyzed. We assessed HPV types using the polymerase chain reaction with E6 consensus primers, hybrid capture assays (high or low risk), and dot blot hybridization of generic E6 PCR products with E6 type-specific oligonucleotide probes. The presence and type of HPV were correlated with patient data from a retrospective chart review. We found that RPs may have either low- or high-risk HPV types and some contain multiple HPV types. Respiratory infection with high-risk HPV apparently introduces a long-term risk of squamous cell carcinoma development, even in the absence of conventional cofactors. Low-risk HPV infection may also act in association with these cofactors to promote carcinogenesis. Our data also show a racial imbalance in RP that may indicate a difference in genetic resistance and/or susceptibility to HPV infection and the development of RP.

Role of human papillomavirus typing in diagnosis and clinical decision making for a giant verrucous genital lesion

A 60-year-old man presented with a 12.0 x 10.0-cm exophytic, verrucous genital plaque. Multiple biopsy specimens were evaluated by standard histologic analysis and polymerase chain reaction assays for human papillomavirus (HPV) deoxyribonucleic acid. All biopsy specimens showed histopathologic changes consistent with giant condyloma of Buschke-Lowenstein (GCBL), were uniformly positive for HPV 6/11, and showed a weaker signal for HPV 16. Published reports suggest that the presence of HPV may be useful in differentiating GCBL from verrucous carcinoma (VC), but absence of "high-risk" HPV types in GCBL cannot exclude focally invasive squamous cell carcinoma. Screening for HPV may be a helpful adjunct in differentiating GCBL from VC, but histopathologic criteria for malignancy should take precedence over HPV typing when determining management.

Effect of HIV infection on the natural history of anal human papillomavirus infection

OBJECTIVE

To identify risk factors for the detection of prevalent and incident anal human papillomavirus (HPV) infection, and HPV persistence among HIV-seropositive and seronegative homosexual men.

DESIGN

Longitudinal study of 287 HIV-seronegative and 322 HIV-seropositive men attending a community-based clinic.

METHODS

Subjects underwent an interview and examination; specimens were collected for HIV serology and assessment of anal HPV and HIV DNA.

RESULTS

Anal HPV DNA was detected at study entry in 91.6% of HIV-infected men, and 65.9% of men not infected with HIV. HPV detection was associated with lifetime number of sexual partners and recent receptive anal intercourse (HIV-seronegative men), decreased CD4+ lymphocyte count (HIV-seropositive men), and anal warts (all men). Among men negative for HPV at study entry, subsequent detection of HPV was associated with HIV, unprotected receptive anal intercourse, and any sexual contact since the last visit. Among men positive for HPV at study entry, subsequent detection of additional HPV types was more common among HIV-seropositive men. Becoming HPV negative during follow-up was less common among men with HIV or high HPV levels at study entry. Among those with HIV, HPV persistence was associated with presence of anal HIV DNA, but not with CD4+ lymphocyte count.

CONCLUSIONS

Risk of anal HPV infection appears to increase with sexual exposure, epithelial trauma, HIV infection and immune deficiency. Incident infection may result from recent sexual exposure or reactivation of latent infection. Further studies are needed to elucidate the mechanism by which HIV DNA in the anal canal increases the risk of HPV persistence.

Low risk of perinatal transmission of human papillomavirus: results from a prospective cohort study

OBJECTIVE

Our purpose was to evaluate the risk of perinatal transmission of human papillomavirus.

STUDY DESIGN

Pregnant women were evaluated at <20 weeks' and between 34 and 36 weeks' gestation for genital human papillomavirus by clinical and colposcopic examination and by polymerase chain reaction. Their 151 infants were evaluated at birth, 6 weeks, and 6, 12, 18, 24, and 36 months of age for detection of human papillomavirus deoxyribonucleic acid by polymerase chain reaction on samples from the mouth, external genitalia, and anus. Polymerase chain reaction was performed with human papillomavirus L1 consensus primers and hybridization to human papillomavirus types 6, 11, 16, 18, 31, 33, 35, 39, and 45 and to a generic probe.

RESULTS

During pregnancy 112 (74%) of 151 women had historic, clinical, or deoxyribonucleic acid evidence of genital human papillomavirus infection. At 479 infant visits, human papillomavirus deoxyribonucleic acid was detected from only five (1.5%) of the 335 genital, four (1.2%) of the 324 anal, and none of the 372 oral or nasopharyngeal specimens. A positively reacting specimen was obtained from three (4%) of 80 infants born to women with human papillomavirus deoxyribonucleic acid detected at 34 weeks' gestation and from five (8%) of 63 born to women without human papillomavirus deoxyribonucleic acid (p = 0.47). All positive results in the infants were positive only with the generic probe and were preceded or followed by negatively reacting specimens. No clinical manifestations of human papillomavirus infection were detected in any infant.

CONCLUSIONS

The isolated detection of unclassified human papillomavirus types from infants at only single visits may represent low-level genital or nongenital human papillomavirus or may represent contamination. Although perinatal transmission of human papillomavirus is not ruled out by these data, the upper 95% confidence interval for detection of perinatal transmission from women with any evidence of genital human papillomavirus was only 2.8%.

Comparison of the hybrid capture tube test and PCR for detection of human papillomavirus DNA in cervical specimens

The strong association of human papillomavirus (HPV) and cervical cancer makes it important to study HPV detection methods that may play a role in cervical cancer screening. We compared two DNA methods that are commonly used for HPV research in the United States: the MY09/MY11 L1 consensus primer PCR-based test and the first-generation Hybrid Capture tube method (HCT). Laboratory assays by each method were performed with 596 cervicovaginal specimens collected from participants in a large cohort study conducted in Portland, Oreg. Included were 499 specimens from women whose cytology was normal and 97 specimens from women with squamous intraepithelial lesions (SILs). The overall HPV DNA positivity for known types was 22.5% by PCR compared to 13.6% by HCT. When the analysis was restricted to the 14 HPV types detectable by both methods, the sensitivity of HCT, with PCR used as the standard for HPV status, was higher for specimens from women with concurrent SILs (81.0%) than for specimens from women with normal cytology (46.7%). Among specimens testing positive by both methods, 97.2% of the time the two methods agreed on whether specimens were positive for cancer-associated HPV types. Both of these HPV test methods provide information that supplements the information provided by the Pap smear. The PCR method has higher analytic sensitivity than HCT in detecting HPV, but HCT may be helpful in identifying women with concurrent SILs.

Genomic variation of human papillomavirus type 16 and risk for high grade cervical intraepithelial neoplasia

BACKGROUND

Epidemiologic studies have demonstrated strong and consistent associations between the detection of human papillomavirus (HPV) type 16 DNA and the risk of cervical intraepithelial neoplasia (CIN) and cervical cancer. However, HPV16 is also the most common type of HPV in the normal population, and only a minority of women with HPV16 infection develop cervical cancer. Studies of genomic heterogeneity in HPV16 have demonstrated the presence of multiple variant forms in all human populations examined to date. It is conceivable that the natural variants of HPV16 in a given population may not have the same biologic behavior.

PURPOSE

This study was designed to determine the association between natural variants of HPV16 and the risk of biopsy-confirmed CIN 2 or 3, the most important precancerous lesions of the uterine cervix.

METHODS

Prospective studies were conducted among 1) women attending a university and 2) women presenting to a sexually transmitted disease clinic. Subjects were eligible for inclusion in this investigation if the initial cytologic findings did not reveal CIN 2-3 and HPV16 DNA was detected by means of a polymerase chain reaction (PCR)-based method in one or more cervical or vulvovaginal samples. Eligible subjects were followed every 4 months with cervical Pap smears and colposcopic examinations. Women were referred for biopsy if cytology or colposcopy suggested CIN 2-3. Two groups of HPV16 variants, prototype-like and nonprototype-like, were determined by means of single-strand conformation polymorphism (SSCP) analysis of PCR products from the noncoding region of the viral genome. Representative SSCP patterns from HPV16 variants were further characterized by direct DNA sequencing of the PCR products. Relative risks (RRs) and 95% confidence intervals (CIs) were calculated by Cox regression analysis.

RESULTS

Prototype-like variants accounted for 79% of the HPV16 detected in university students and 86% of the virus detected in patients presenting to the sexually transmitted disease clinic. CIN 2-3 was confirmed by biopsy in nine of 57 HPV16-positive women attending the university and in 10 of 66 HPV16-positive women presenting to the sexually transmitted disease clinic. Among university students, those with HPV16 nonprototype-like variants were 6.5 (95% CI = 1.6-27.2) times more likely to develop CIN 2-3 than those with prototype-like variants. A similar association was observed among women presenting to the sexually transmitted disease clinic (RR = 4.5; 95% CI = 0.9-23.8).

CONCLUSIONS

This study suggests that the risk of developing CIN 2-3 is not the same with all variants of HPV16 and that nonprototype-like variants confer a greater risk compared with prototype-like variants. The important genomic differences underlying this increased risk of CIN 2-3 remain to be determined.

PCR detection of human papillomavirus: comparison between MY09/MY11 and GP5+/GP6+ primer systems

Human papillomavirus (HPV) is an etiologic agent of cervical cancer and is the most common sexually transmitted disease in women. PCR amplification of HPV genomes is the most sensitive method for the detection of cervicovaginal HPV. We have compared the two most commonly used PCR primer sets, MY09/MY11 (MY-PCR) and GP5+/GP6+ (GP+-PCR), for the detection of HPV DNA in cervicovaginal lavage samples from 208 women. Oligonucleotide probes for 39 different HPV types were used. Both primer sets amplified a wide spectrum of HPV genotypes and detected similar overall prevalences of 45% (94 of 208) and 43% (89 of 208), respectively. The MY-PCR system detected 27 of 30 (90%) samples with multiple HPV types, whereas the GP+-PCR system detected 14 of 30 (47%) samples with multiple HPV types. Differences in the detection of HPV types 35, 53, and 61 were noted between the two primer systems. Serial dilution of plasmid templates indicated a 3-log decrease in the amplification of HPV type 35 by MY-PCR and HPV types 53 and 61 by GP+-PCR. These results indicate that although the MY-PCR and GP+-PCR identified nearly equivalent prevalences of HPV in a set of clinical samples, differences in the detection of specific types and infections with multiple types were found. Differences in the sensitivities and characteristics of the PCR systems for the detection of HPV within clinical samples should be considered when comparing data between studies and/or in designing new studies or clinical trials.

Diagnosis of human papillomavirus genital tract infection

Although visible anogenital lesions are present in some persons infected with human papillomavirus (HPV), the majority of individuals with HPV genital tract infection do not have clinically apparent disease. Conventional viral detection assays, including serologic assays and growth in cell culture, are not available for the diagnosis and tracking of HPV infection. Papanicolaou tests are a valuable screening tool, but they miss a large proportion of HPV-infected persons. Accordingly, HPV DNA detection assays have become a key research tool in the detection of HPV infection, particularly in asymptomatic individuals. Several types of HPV DNA tests are now available, including Southern blots, dot blots, in situ hybridization, polymerase chain reaction, and solution hybridization (Hybrid Capture assay). Of these, the polymerase chain reaction assay is the most sensitive, whereas dot blots and solution hybridization are the least labor intensive. HPV DNA detection assays are not routinely used in screening patients, in part because the clinical relevance of asymptomatic infection is unclear. Nevertheless, these tests may be beneficial in confirming differential diagnoses and in providing prognostic information, particularly with respect to the HPV type involved.

A sensitive, type-specific, fluorogenic probe assay for detection of human papillomavirus DNA

A simple method for the detection of a number of human papillomavirus (HPV) genotypes associated with cervical cancer has been developed. The assay exploits the 5'-->3' exonucleolytic activity of Taq DNA polymerase to increase the signal from fluorescent dyes by releasing them from genotype-specific probes during PCR. The probes are oligonucleotides with a 5' reporter dye (6-carboxyfluorescein), a quencher dye (6-carboxy-tetramethyl-rhodamine), and a phosphate-blocked 3' end. In the intact probe, the proximity of the reporter and the quencher results in suppression of reporter fluorescence by Förster-type energy transfer (V. T. Förster. Ann. Phys. 2:55-75, 1948). If the probe is bound downstream of either primer during PCR, the 5'-->3' exonucleolytic activity of Taq polymerase degrades it, allowing the reporter to diffuse away from the quencher, which results in an increase in reporter fluorescence. The increased fluorescence is directly related to the amount of target DNA and can be detected with an automated fluorometer. Probes for the L1 region of the cervical-cancer-associated HPV types 16, 18, 31, 33, and 35 were synthesized and the assays were optimized. The most sensitive assay can detect as few as two copies of HPV DNA in human cervical specimens.

Generation of DNA probes for detection of microorganisms by polymerase chain reaction fingerprinting

Identification of medically relevant microorganisms is important for diagnosis, treatment and prevention of infectious diseases. This has initiated the development of a large number of identification and typing techniques based on phenotypic and genetic characteristics. In general, these last mentioned nucleic acid-mediated techniques provide more detailed and consistent information on strain-specific characteristics. However, the development of clinically useful microbial DNA/RNA probes requires nucleotide sequence information and a set of well defined reference organisms for test validation in comparison with the current gold standard. This is a requirement for the development of accurate nucleic acid hybridisation and/or amplification tests. Recently, it has been demonstrated that polymerase chain reaction (PCR)-mediated genetic typing of microorganisms can lead to the immediate isolation of species-specific DNA probes by comparison of DNA fingerprints. This combines the sensitivity of PCR with the specificity of DNA probing without the need to generate nucleic acid sequence information prior to probe development. The implications of this procedure for clinical microbiology and epidemiological surveillance will be discussed. It is shown that specific probes can be developed for various taxonomic levels and that detection and identification can be combined into a single, fast procedure. The versatility and widely applicable principles of this procedure will be highlighted and exemplified by some newly developed tests and a review of the current literature.

Laboratory diagnosis of chancroid using species-specific primers from Haemophilus ducreyi groEL and the polymerase chain reaction

To enhance laboratory identification of Haemophilus ducreyi, the causative agent of the genital ulcer disease chancroid, a polymerase chain reaction (PCR) assay was developed using target DNA sequences from the essential H. ducreyi gene, groEL. Positive reactions were obtained in this PCR assay with 139 isolates of H. ducreyi from patients in worldwide locations from the 1940s to the 1990s. In contrast, 24 other bacterial species were negative. When genital ulcer specimens from 162 African patients with clinically diagnosed chancroid were evaluated, 66 were culture positive. The sensitivity of PCR as compared with culture was 89% (59 of 66), and specificity was 79% (76 of 96). However, representative samples of the 20 culture-negative, PCR-positive specimens were confirmed as positive by a second PCR assay using different H. ducreyi-specific primers. Thus, combined results of culture and PCR detected H. ducreyi in 86 specimens, with resolved sensitivities of 92% (79 of 86) for PCR, and 77% (66 of 86) for culture. These results suggest that PCR assays for H. ducreyi have great potential for augmenting or replacing problematic cultural techniques.

Cancer associated human papillomaviruses: perinatal transmission and persistence

OBJECTIVE

To demonstrate the perinatal transmission and persistence of the cancer associated human papillomavirus types 16, 18, 31 and 33.

DESIGN

Cervical swabs were taken from pregnant women between 20 and 38 weeks of gestation. Buccal and genital swabs were taken from infants at 24 h and at six weeks after delivery and examined for HPV-16, -18, -31 and -33 DNA by the polymerase chain reaction.

SETTING

Maternity Unit at St Thomas's Hospital, London.

SUBJECTS

Thirty-one pregnant women, 16 with a previous history of cervical intraepithelial neoplasia or genital warts, or both, and their 32 infants (one set of twins).

RESULTS

Twenty of the 31 (65%) women were positive for HPV-DNA prior to delivery. Twelve of 32 (38%) and eight of 31 (26%) infants were HPV-DNA positive at 24 h and six weeks respectively. Swabs taken at 24 h demonstrated HPV type 16 in five mother-infant pairs and HPV type 18 in two mother-infant pairs. Dual infections with HPV types 16 and 18 were demonstrated in swabs from three mother-infant pairs. At six weeks, HPV-16 was demonstrated in swabs from six infants and HPV-18 in swabs from two infants.

CONCLUSIONS

Perinatal transmission of human papillomavirus types 16 and 18 occurred in 55% cases. Persistent human papillomavirus infection was demonstrated at six weeks of age. Whether acquisition of human papillomavirus during the perinatal period predisposes to an increased risk of cervical intraepithelial neoplasia among female infants in later life remains to be established. Information on the persistence of perinatally acquired human papillomavirus is required before rational vaccination programmes can be considered.

DNA fingerprinting of medically important microorganisms by use of PCR

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.

Interlaboratory agreement study of a double set of PCR plasmid primers for detection of Chlamydia trachomatis in a variety of genitourinary specimens

We conducted a tricenter interlaboratory agreement study to assess the agreement of PCR results obtained for detection of Chlamydia trachomatis in genitourinary specimens. A total of 120 specimens (49 positive and 71 negative), including 20 first-void urine samples, 50 endocervical and 50 urethral swabs (40 males), were coded and sent from a reference laboratory (laboratory A) to two other laboratories. Laboratories B and C were provided with a standardized protocol and reagent package including two sets of plasmid PCR primers (KL1-KL2 and T1-T2) and were asked to test each specimen with the first set of primers (KL1-KL2) and to confirm positives with the second set of primers (T1-T2). Laboratory B identified 47 of 49 positives and 69 of 70 negatives (one specimen dried up on shipping) following the initial PCR, for an accuracy of 97.5% (116 of 119), and 47 of 49 positives and 70 of 70 negatives after confirmatory testing of the positives, for an accuracy of 98.3% (117 of 119). Laboratory C identified 42 of 49 positives and 70 of 70 negatives for the initial PCR, for an accuracy of 94.1% (112 of 119), and 39 of 42 positives and 70 of 70 negatives for the confirmatory PCR, for an accuracy of 91.6% (109 of 119). The overall accuracy of PCR testing was 96.6% (345 of 357). The kappa agreement statistics for agreement between pairs of laboratories after confirmation of positives were 0.97 for laboratories A and B, 0.83 for laboratories B and C, and 0.83 for laboratories A and C. Use of the confirmatory PCR improved the specificity and overall accuracy of results for individual laboratories but reduced slightly the results obtained for agreement between laboratories. These results demonstrate that when standardized reagents and protocols are used, PCR results are highly reproducible and excellent agreement between laboratories is obtainable.