Janel Dockter

Highly Sensitive Multiplex Assay for Detection of Human Immunodeficiency Virus Type 1 and Hepatitis C Virus RNA

ABSTRACT Various nucleic acid assays have been developed and implemented for diagnostics and therapeutic monitoring of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections. The high-throughput, semiautomated assays described here were developed to provide a method suitable for screening plasma specimens for the presence of HIV-1 and HCV RNAs. Three assays were developed: a multiplex HIV-1/HCV assay for simultaneous detection of HIV-1 and HCV, and discriminatory assays for specific detection of HIV-1 and HCV. The assay systems utilize three proprietary technologies: (i) target capture-based sample preparation, (ii) transcription-mediated amplification (TMA), and (iii) hybridization protection assay (HPA). An internal control is incorporated into each reaction to control for every step of the assay and identify random false-negative reactions. The assays demonstrated a sensitivity of at least 100 copies/ml for each target, and they detected with similar sensitivity all major variants of HCV and HIV-1, including HIV-1 group O strains. Assay sensitivity for one virus was not affected by the presence of the other. The specificity of these TMA-driven assays was ≥99.5% in both normal donor specimens and plasma containing potentially interfering substances or other blood-borne pathogens. Statistical receiver operating characteristic plots of 1 − specificity versus sensitivity data determined very wide analyte cutoff values for each assay at the point at which the assay specificity and sensitivity were both ≥99.5%. The sensitivity, specificity, and throughput capability predict that these assays will be valuable for large-volume plasma screening, either in a blood bank setting or in other diagnostic applications.

A cross-sectional study of a prototype carcinogenic human papillomavirus E6/E7 messenger RNA assay for detection of cervical precancer and cancer.

Purpose: To evaluate carcinogenic human papillomavirus (HPV) mRNA for E6 and E7 mRNA detection on clinical specimens to identify women with cervical precancer and cancer. Experimental Design: We evaluated a prototype assay that collectively detects oncogenes E6/E7 mRNA for 14 carcinogenic HPV genotypes on a sample of liquid cytology specimens (n = 531), masked to clinical data and to the presence of HPV genotypes detected by PGMY09/11 L1 consensus primer PCR assay. Results: We found an increasing likelihood of testing positive for carcinogenic HPV E6/E7 mRNA with increasing severity of cytology (PTrend < 0.0001) and histology (PTrend < 0.0001), with 94% of cervical intraepithelial neoplasia grade 3 (CIN3) histology cases (46 of 49) and all five cancer cases testing positive for carcinogenic HPV E6/E7 mRNA. Overall, fewer specimens tested positive for carcinogenic HPV E6/E7 mRNA than for carcinogenic HPV DNA (P < 0.0001, McNemars χ2 test), especially in women with <CIN1 (P < 0.0001). We also found that using a higher positive cutpoint for detection of carcinogenic HPV E6/E7 mRNA improved the association of positive test results with cervical precancer and cancer by reducing the number of test positives in women without precancer without reducing clinical sensitivity for cervical precancer and cancer compared with detection of carcinogenic HPV E6/E7 mRNA using a lower positive cutpoint by the same assay and with detection of carcinogenic HPV DNA. Conclusions: We found that carcinogenic HPV E6/E7 mRNA is a potentially useful biomarker for detection of cervical precancer and cancer and warrants further evaluation.

Clinical performance of the APTIMA ® HPV Assay for the detection of high-risk HPV and high-grade cervical lesions

BACKGROUND Human papillomavirus (HPV) DNA testing is widely used in conjunction with Papanicolaou (Pap) testing in cervical cancer screening programs to improve the detection of high-grade lesions. While HPV DNA test sensitivity is good, an improvement in specificity is desired. Detection of HPV mRNA may improve specificity. The APTIMA HPV Assay detects the mRNA of 14 high-risk HPV types in liquid-based cytology specimens. OBJECTIVE To evaluate APTIMA HPV Assay performance for detection of high-risk HPV and high-grade cervical intraepithelial neoplasia (CIN) compared to Qiagens Hybrid Capture 2 HPV DNA (HC2) test. STUDY DESIGN Liquid Pap specimens were collected from 800 women referred to colposcopy and tested with the APTIMA HPV Assay and the HC2 test. Complete results were available for 753 subjects. A subset of samples (n = 393) were typed using Roches Linear Array HPV Genotyping Test. RESULTS Sensitivity and specificity for detection of high-risk HPV were >92% and 99% for the APTIMA HPV Assay and 93% and 82% for the HC2 test. Clinical sensitivity and specificity were 91% and >55% for detection of CIN 2+, and 98% and 53% for detection of CIN 3+ for the APTIMA HPV Assay; values for the HC2 test were 95% and 47% for CIN 2+, and 99% and 44% for CIN 3+. CONCLUSIONS The APTIMA HPV Assay is sensitive and very specific for detection of high-risk HPV. The APTIMA HPV Assay had similar clinical sensitivity for disease detection but higher clinical specificity than the HC2 test, which may improve patient management and reduce the cost of care.

PREVALENCE, RISK FACTORS, AND OUTCOMES FOR OCCULT HEPATITIS B VIRUS INFECTION AMONG HIV-INFECTED PATIENTS

Background:Occult hepatitis B virus (HBV) is defined by the presence of HBV DNA in individuals with HBV core antibodies (anti-HBc) but without HBV surface antigen (HBsAg). The prevalence of occult HBV in HIV-infected patients remains controversial, and the risk factors and clinical significance are unknown. Objectives:To determine the prevalence, risk factors, and clinical significance of occult HBV among HIV-infected patients. Hypothesized risk factors include chronic hepatitis C virus (HCV), CD4 count <200 cells/mm3, HIV RNA level >1000 copies/mL, and lack of use of anti-HBV antiretrovirals. Methods:We examined randomly selected HBsAg−/anti-HBc+ HIV-infected patients in the Penn Center for AIDS Research Adult/Adolescent Database and Specimen Repository. HBV DNA was qualitatively detected using a transcription-mediated amplification assay. Risk factors and transaminases were ascertained at the time sera were collected. Results:A total of 699 HBsAg−/anti-HBc+ HIV-infected patients were identified. Of 179 randomly selected subjects, 17 (10%; 95% confidence interval [CI]: 5% to 14%) had occult HBV. Differences in the prevalence of HBV surface antibody (anti-HBs) between those with (7 [41%]) and without (94 [58%]) occult HBV were not statistically significant (P = 0.3). An HIV RNA level >1000 copies/mL (adjusted odds ratio [OR] = 4.88, 95% CI: 1.01 to 30.26) and the absence of chronic HCV (adjusted OR = 0.26, 95% CI: 0.05 to 0.95) were associated with occult HBV. Occult HBV did not increase the risk of transaminitis (adjusted OR = 0.42, 95% CI: 0.12 to 1.45). Conclusions:Occult HBV occurred in a sizable proportion of HIV-infected patients and was associated with detectable HIV and the absence of chronic HCV. It did not increase the risk of transaminitis. The presence of anti-HBs does not rule out occult HBV. Future studies should examine the long-term clinical implications of occult HBV in HIV-infected patients.

Analytical characterization of the APTIMA® HPV Assay

BACKGROUND Human papillomavirus (HPV) testing has improved the sensitivity for the detection of cervical pre-cancer and cancer as compared to Pap testing. Several HPV tests are commercially available and most target the DNA from 13 or 14 high-risk HPV types. The APTIMA HPV Assay however, detects HPV E6/E7 mRNA from 14 high-risk types of HPV: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68. OBJECTIVE To determine the analytical performance characteristics of the APTIMA HPV Assay. STUDY DESIGN Analytical sensitivity, analytical specificity, reproducibility, and the effect of potentially interfering substances was determined for the APTIMA HPV Assay on both the DTS (semi-automated) and TIGRIS DTS (fully automated) systems. RESULTS The 95% detection limit for both systems was between 17 and 488 copies/reaction, depending on the HPV type. The assay did not cross-react with normal flora and opportunistic organisms that may be found in cervical samples, or low-risk HPV types. Spermicides, anti-fungal and anti-itch medications, whole blood, glacial acetic acid, and most lubricants did not interfere with assay performance. Those lubricants containing polyquaternium 15 did interfere with assay performance. Inter-instrument, inter-operator, inter-lot, and inter-run signal variability were <10% for >99% of the data. Intra-run variability was <15%, except for those samples with concentrations at or below the 95% detection limit of the assay. CONCLUSIONS Based upon the analytical sensitivity, analytical specificity, and low variability, the APTIMA HPV Assay showed excellent performance and robustness.

Significant Closure of the Human Immunodeficiency Virus Type 1 and Hepatitis C Virus Preseroconversion Detection Windows with a Transcription-Mediated-Amplification-Driven Assay

ABSTRACT While the present generation of serology-based assays has significantly decreased the number of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections acquired by transfusion, the possibility of infected donations escaping detection still exists. The average seronegative viremic window duration during which immunological assays are unable to detect the virus is estimated to be between 16 and 22 days for HIV-1 and approximately 70 days for HCV. Significant reduction of detection window duration was demonstrated using a nucleic acid amplification assay, the Procleix HIV-1/HCV Assay, which utilizes transcription-mediated amplification technology to simultaneously detect HIV-1 and HCV RNAs. For 26 commercially available HIV-1 seroconversion panels tested, specimens were reactive in the HIV-1/HCV assay at the same time as or earlier than in serological assays. Overall, the HIV-1/HCV assay was able to reduce the detection window duration by an average of 14 days and 6 days compared to tests relying on recognition of HIV-1 antibody and p24 antigen, respectively. For 24 commercially available HCV seroconversion panels tested, the specimens were reactive in the HIV-1/HCV assay at an earlier blood sampling date than in serological assays, reducing the detection window duration by an average of 26 days. Similar results were obtained in testing the HIV-1 and HCV seroconversion panels in the virus-specific HIV-1- and HCV-discriminatory assays, respectively. In conclusion, the HIV-1/HCV assay and corresponding discriminatory assays significantly reduced detection window durations compared to immunoassays.

APTIMA HPV assay performance in women with atypical squamous cells of undetermined significance cytology results

OBJECTIVE The objective of the study was to determine the sensitivity and specificity of the APTIMA human papillomavirus (AHPV) assay for high-grade cervical intraepithelial neoplasia (CIN) in women 21 years old and older with atypical squamous cells of undetermined significance (ASC-US) cytology. STUDY DESIGN Women 21 years old and older with ASC-US cytology had colposcopy/biopsy and molecular human papillomavirus testing. Performance of the AHPV and Hybrid Capture 2 assays was compared with a clinical diagnosis of CIN grade 2, CIN grade 3, or adenocarcinoma in situ (CIN2 or greater). RESULTS Of 939 evaluable subjects, CIN2 or greater and CIN3 or greater prevalence was 9.7% and 4.4%, respectively. AHPV sensitivity and specificity was 86.8% and 62.9% for CIN2 or greater detection and 90.2% and 60.2% for CIN3 or greater, respectively. AHPV had a similar sensitivity to Hybrid Capture 2 but a significantly higher specificity (62.9% vs 55.8%, P < .001) for CIN2 or greater detection. CONCLUSION Among women with ASC-US cytology, detection of high-risk human papillomavirus E6/E7 oncogenic messenger ribonucleic acid is an effective triage method for colposcopy referral.

The course of hepatitis C viraemia in transfusion recipients prior to availability of antiviral therapy.

Summary.  Knowing the likely distribution of intervals from hepatitis C infection to first RNA‐negativity is important in deciding about therapeutic intervention. Prospectively collected sera and data from the Transfusion‐transmitted Viruses Study (1974–1980) provide specific dates of infection and pattern of alanine aminotransferase (ALT) elevations. We examined frequency, timing and correlates of spontaneous resolution for 94 acutely infected transfusion recipients followed for a median of 9.5 months. Later, follow‐up sera (>10 years) were available for 27 of the 94 cases from a Veterans Administration (VA) Study (1989–1990). Twenty‐five (27%) of the 94 cases were classified as probably resolved during the episode itself. First RNA negativity occurred at 6–50 weeks (median, 19.5 weeks) after infection, and 5–43 weeks (median, 11 weeks) after ALT elevation. Thirteen of the 25 cases remained RNA‐negative subsequently; 12 others had 1–6 RNA‐positive sera intercalated between first and last RNA‐negative results. RNA negativity, therefore, began variably and was interrupted in 12 cases of 25 (48%) by transient RNA‐positive sera. Five of these 25 patients who were RNA‐negative in the last study specimen had late, Veterans Administration Study follow‐up; none showed viraemia. Of the remaining 69 transfusion transmitted virus study recipients, whose last serum was RNA‐positive, two cleared viraemia after the last study serum but before late follow‐up. Eleven (16%) had 23 intercalated RNA‐negative sera before last positivity. RNA status, therefore, needs monitoring for many months before judging the spontaneous outcome as transient negativity may occur. Resolution was significantly more common in women and symptomatic cases; it was not associated with viral load in the infectious donation, HCV genotype, or the recipient’s age.

Efficiency of the APTIMA® HPV Assay for detection of HPV RNA and DNA targets

BACKGROUND The APTIMA HPV Assay (AHPV) is designed to detect HPV E6/E7 mRNA from 14 high-risk types in Cytyc PreservCyt liquid-based cytology specimens. OBJECTIVES To compare AHPV analytical sensitivity for RNA and DNA; to compare the sensitivity of AHPV and Hybrid Capture 2 (HC2) assays for HPV DNA detection; to compare assay performance with and without sample denaturation; to compare assay results with cytology. STUDY DESIGN Analytical sensitivity of AHPV for detecting E6/E7 RNA was assessed by spiking samples with various quantities of HPV 16 E6/E7 in vitro RNA transcript or HPV 16-positive SiHa cells. AHPV and HC2 analytical sensitivity for HPV 16 DNA was evaluated by spiking samples with various quantities of a plasmid vector containing cloned HPV 16 DNA, or with purified SiHa cell genomic DNA containing integrated HPV 16 genome. Samples were tested using standard AHPV and HC2 protocols. Endocervical samples from 568 women were collected in Digene Specimen Transport Medium. Non-denatured and denatured samples were tested in AHPV and denatured samples with HC2. Assay results were compared to each other, and to cytology. RESULTS AHPV had substantially higher (2 4 log(10)) analytical sensitivity for HPV 16 RNA than for HPV 16 DNA. AHPV also had substantially lower (3 log(10)) analytical sensitivity for HPV 16 DNA compared to HC2. The overall agreement between assay results in clinical specimens was 94.2%, but AHPV had fewer positives than HC2 (48.4% positive agreement). In denatured samples, the number of samples testing positive in AHPV increased two-fold, yielding a positive agreement rate of 88.7%. When assay results were compared with cytology, AHPV had fewer positives in samples with normal or ASC-US diagnoses than did HC2. CONCLUSIONS AHPV is much more efficient at detecting HPV 16 RNA than DNA. Selective capture, amplification, and detection of HPV RNA by AHPV may improve the specificity of molecular HPV testing.

Sensitive detection of genetic variants of HIV-1 and HCV with an HIV-1/HCV assay based on transcription-mediated amplification

This paper describes a comprehensive study of hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) genotype sensitivity of the transcription-mediated amplification (TMA)-based HIV-1/HCV assay, developed and manufactured by Gen-Probe Incorporated (San Diego, CA) for screening human plasma specimens in blood bank settings. The TMA HIV-1/HCV assay is a qualitative, in vitro nucleic acid testing system used for initial screening. HIV-1 and HCV discriminatory assays are used to distinguish between HIV-1 and HCV infection or co-infection. In this study, multiple unique specimens representing HCV genotypes 1-6 were tested at various dilutions. The results show that the TMA HIV-1/HCV assay and the TMA HCV discriminatory assay have similar HCV genotype sensitivity, as both assays detected all six genotypes at 100 copies/ml and nearly all replicates tested at 30 copies/ml. Similarly, numerous unique specimens representing HIV-1 group M subtypes (A-G), HIV-1 group N, and group O specimens were tested at various dilutions. The TMA HIV-1/HCV assay and the TMA HIV-1 discriminatory assay were found to have similar HIV-1 subtype sensitivity; all variants at 100 copies/ml and nearly all at 30 copies/ml were detected. These results indicate that the TMA assays meet the sensitivity requirements for blood screening in blood banks worldwide.