External quality assessment program for qualitative and quantitative detection of hepatitis C virus RNA in diagnostic virology

Use of a Novel Virus Inactivation Method for a Multicenter Avian Influenza Real-Time Reverse Transcriptase—Polymerase Chain Reaction Proficiency Study

Proficiency assessments are important elements in quality control for diagnostic laboratories. Traditionally, proficiency testing for polymerase chain reaction (PCR)–based assays has involved the use of clinical samples, samples “spiked” with live agents or DNA plasmids. Because of government regulations and biosecurity concerns, distribution of live high-consequence pathogens of livestock and poultry, such as avian influenza, is not possible, and DNA plasmids are not technically suitable for evaluating RNA virus detection. Therefore, a proficiency testing panel using whole avian influenza in a diluent containing a phenolic disinfectant that inactivates the virus while preserving the RNA for at least 8 weeks at −70 C was developed and used in a multicenter proficiency assessment for a type A influenza real-time reverse transcriptase (RT)–PCR test. The test, which was highly standardized, except for variation in the real-time RT-PCR equipment used, was shown to be highly reproducible by proficiency testing in 12 laboratories in the United States, Canada, and Hong Kong. Variation in cycle threshold values among 35 data sets and 490 samples was minimal (CV = 5.19%), and sample identifications were highly accurate (96.7% correct identifications) regardless of real-time PCR instrumentation.

Ring test evaluation of the detection of influenza A virus in swine oral fluids by real-time reverse-transcription polymerase chain reaction and virus isolation

The probability of detecting influenza A virus (IAV) in oral fluid (OF) specimens was calculated for each of 13 assays based on real-time reverse-transcription polymerase chain reaction (rRT-PCR) and 7 assays based on virus isolation (VI). The OF specimens were inoculated with H1N1 or H3N2 IAV and serially diluted 10-fold (10(-1) to 10(-8)). Eight participating laboratories received 180 randomized OF samples (10 replicates × 8 dilutions × 2 IAV subtypes plus 20 IAV-negative samples) and performed the rRT-PCR and VI procedure(s) of their choice. Analysis of the results with a mixed-effect logistic-regression model identified dilution and assay as variables significant (P < 0.0001) for IAV detection in OF by rRT-PCR or VI. Virus subtype was not significant for IAV detection by either rRT-PCR (P = 0.457) or VI (P = 0.101). For rRT-PCR the cycle threshold (Ct) values increased consistently with dilution but varied widely. Therefore, it was not possible to predict VI success on the basis of Ct values. The success of VI was inversely related to the dilution of the sample; the assay was generally unsuccessful at lower virus concentrations. Successful swine health monitoring and disease surveillance require assays with consistent performance, but significant differences in reproducibility were observed among the assays evaluated.

Sequence Variation in Amplification Target Genes and Standards Influences Interlaboratory Comparison of BK Virus DNA Load Measurement

International guidelines define a BK virus (BKV) load of ≥4 log10 copies/ml as presumptive of BKV-associated nephropathy (BKVN) and a cutoff for therapeutic intervention. To investigate whether BKV DNA loads (BKVL) are comparable between laboratories, 2 panels of 15 and 8 clinical specimens (urine, whole blood, and plasma) harboring different BKV genotypes were distributed to 20 and 27 French hospital centers in 2013 and 2014, respectively. Although 68% of the reported results fell within the acceptable range of the expected result ±0.5 log10, the interlaboratory variation ranged from 1.32 to 5.55 log10. Polymorphisms specific to BKV genotypes II and IV, namely, the number and position of mutations in amplification target genes and/or deletion in standards, arose as major sources of interlaboratory disagreements. The diversity of DNA purification methods also contributed to the interlaboratory variability, in particular for urine samples. Our data strongly suggest that (i) commercial external quality controls for BKVL assessment should include all major BKV genotypes to allow a correct evaluation of BKV assays, and (ii) the BKV sequence of commercial standards should be provided to users to verify the absence of mismatches with the primers and probes of their BKV assays. Finally, the optimization of primer and probe design and standardization of DNA extraction methods may substantially decrease interlaboratory variability and allow interinstitutional studies to define a universal cutoff for presumptive BKVN and, ultimately, ensure adequate patient care.

Standardization of NAT for Blood-Borne Pathogens

Assays based on nucleic acid amplification technology (NAT) are increasingly used for screening of blood and for diagnosis or monitoring of patients. Both regulatory requirements for blood screening and international recommendations for the treatment of patients are based on common reference materials available globally for the standardization of NAT assays. World Health Organization International Standards (WHO ISs) and International Reference Panels (WHO IRPs) are primary reference materials. The characterization and manufacture of WHO reference materials as well as their evaluation is performed on behalf of the WHO by collaborating centers; their establishment is decided upon by the WHO Expert Committee on Biological Standardization (ECBS). The potency of the first WHO IS is defined by the 'international unit' (IU) which should be maintained upon replacement of the IS. The IU, unlike copy number or genome equivalent, is defined by the IS with a physical existence, is available worldwide, and allows traceability and comparability of results. The anticipated use of WHO ISs is the calibration of secondary standards or the validation of essential assay features, e.g. limit of detection.

Toward standardization of BK virus monitoring: evaluation of the BK virus R-gene kit for quantification of BK viral load in urine, whole-blood, and plasma specimens

Screening of BK virus (BKV) replication is recommended to identify patients at increased risk of BKV-associated diseases. However, the heterogeneity of molecular techniques hinders the establishment of universal guidelines for BKV monitoring. Here we aimed to compare the performance of the CE-marked BK virus R-gene kit (R-gene) to the performance of our in-house assay for quantification of BKV DNA loads (BKVL). A 12-specimen panel from the Quality Control for Molecular Diagnostics (QCMD) organization, 163 urine samples, and 88 paired specimens of plasma and whole blood (WB) from transplant recipients were tested. Both the R-gene and in-house assays showed a good correlation within the QCMD panel (r = 0.995 and r = 0.989, respectively). BKVL were highly correlated between assays, although positive biases were observed with the in-house assay in analysis of urine (0.72 ± 0.83 log10 copies/ml), plasma (1.17 ± 0.63 log10 copies/ml), and WB (1.28 ± 0.37 log10 copies/ml). Recalibration with a common calibrator significantly reduced the bias in comparisons between assays. In contrast, BKVL was underestimated with the in-house PCR in eight samples containing BKV genotype II, presenting point mutations at primer-annealing sites. Using the R-gene assay, plasma and WB specimens were found to be equally suitable for quantification of BKVL, as indicated by the high correlation coefficient (r = 0.965, P < 0.0001). In conclusion, the R-gene assay demonstrated reliable performance and higher accuracy than the in-house assay for quantification of BKVL in urine and blood specimens. Screening of BKV replication by a well-validated commercial kit may enable clinical laboratories to assess viral loads with greater reproducibility and precision.

External quality assurance of malaria nucleic acid testing for clinical trials and eradication surveillance

Nucleic acid testing (NAT) for malaria parasites is an increasingly recommended diagnostic endpoint in clinical trials of vaccine and drug candidates and is also important in surveillance of malaria control and elimination efforts. A variety of reported NAT assays have been described, yet no formal external quality assurance (EQA) program provides validation for the assays in use. Here, we report results of an EQA exercise for malaria NAT assays. Among five centers conducting controlled human malaria infection trials, all centers achieved 100% specificity and demonstrated limits of detection consistent with each laboratory's pre-stated expectations. Quantitative bias of reported results compared to expected results was generally <0.5 log₁₀ parasites/mL except for one laboratory where the EQA effort identified likely reasons for a general quantitative shift. The within-laboratory variation for all assays was low at <10% coefficient of variation across a range of parasite densities. Based on this study, we propose to create a Molecular Malaria Quality Assessment program that fulfills the need for EQA of malaria NAT assays worldwide.

Hepatitis C virus infection of human cytotrophoblasts cultured in vitro

Hepatitis C virus (HCV) infection in the uterus is a significant path of vertical HCV transmission. Some studies consider vertical HCV transmission in the uterus as the result of maternal blood leakage into infant blood, whereas others theorize that HCV is transmitted by the mother to the infant through cells constituting the placenta barrier. Although trophoblasts play an important role in the placenta barrier, no definitive evidence has been presented to prove that cytotrophoblasts can be infected with HCV. The current study investigated whether or not these can be infected with HCV by conducting an experiment, in which cultured human cytotrophoblasts were infected with HCV in vitro. The results were analyzed using reverse transcription polymerase chain reaction (RT-PCR), ultrastructural characteristic changes under an electron microscope, and immunoelectron microscopy. HCV RNA in the supernatant of the cultured medium of the infected group was intermittently detected during the 16-day incubation period using RT-PCR. Under an electron microscope, the ultrastructures of infected human cytotrophoblasts were markedly different from normal cells, demonstrating lysosomal hyperplasia, rough endoplasmic reticulum, decreased lipid droplets, presence of vacuoles, and the appearance of HCV-like particles. Using immunoelectron microscopy, HCV-like particles conjoined with golden granules were also observed. Based on the data, the current study concludes that HCV infects a human cytotrophoblast cultured in vitro; moreover, its ultrastructure changes dramatically upon infection.

International standards and reference materials for quantitative molecular infectious disease testing

The utility of quantitative molecular diagnostics for patient management depends on the ability to relate patient results to prior results or to absolute values in clinical practice guidelines. To do this, those results need to be comparable across time and methods, either by producing the same value across methods and test versions or by using reliable and stable conversions. Universally available standards and reference materials specific to quantitative molecular technologies are critical to this process but are few in number. This review describes recent history in the establishment of international standards for nucleic acid test development, organizations involved in current efforts, and future issues and initiatives.

Quantification of hepatitis C virus (HCV) RNA in a multicenter study: implications for management of HCV genotype 1-infected patients

Assessment of the viral load in hepatitis C virus (HCV) genotype 1-infected patients is critical before, during, and after antiviral therapy. In patients achieving a rapid virological response at week 4 of treatment, the viral load at the baseline is considered a predictive criterion of a sustained virological response 24 weeks after the discontinuation of treatment. A >or=2-log(10) drop in the viral load at week 12 of treatment (early virological response) triggers the continuation of therapy. We organized a multicenter study (MS) for diagnostic laboratories involved in the quantification of HCV RNA. Commercial assays, including two based on real-time reverse transcription-PCR (TaqMan system), and in-house methods, were used by the 61 participants. The overall reproducibility of the commercial quantitative nucleic acid amplification techniques (qNAT) was acceptable. As the intermethod variability among commercial qNAT for HCV RNA was still present, the manufacturers of these test kits should join efforts to harmonize the means of quantification of HCV RNA. This study also shows that caution should be exercised when the baseline viral load is evaluated and when the 2-log(10) reduction after 12 weeks of therapy is interpreted. Finally, this MS confirms the higher sensitivity of the commercial qNAT based on the TaqMan system, making them the elective assays for the monitoring of therapy.

TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories

The TREAT Asia (Therapeutics, Research, Education, and AIDS Training in Asia) Network is building capacity for Human Immunodeficiency Virus Type-1 (HIV-1) drug resistance testing in the region. The objective of the TREAT Asia Quality Assessment Scheme - designated TAQAS - is to standardize HIV-1 genotypic resistance testing (HIV genotyping) among laboratories to permit rigorous comparison of results from different clinics and testing centres. TAQAS has evaluated three panels of HIV-1-positive plasma from clinical material or low-passage, culture supernatant for up to 10 Asian laboratories. Laboratory participants used their standard protocols to perform HIV genotyping. Assessment was in comparison to a target genotype derived from all participants and the reference laboratory's result. Agreement between most participants at the edited nucleotide sequence level was high (>98%). Most participants performed to the reference laboratory standard in detection of drug resistance mutations (DRMs). However, there was variation in the detection of nucleotide mixtures (0-83%) and a significant correlation with the detection of DRMs (p<0.01). Interpretation of antiretroviral resistance showed approximately 70% agreement among participants when different interpretation systems were used but >90% agreement with a common interpretation system, within the Stanford University Drug Resistance Database. Using the principles of external quality assessment and a reference laboratory, TAQAS has demonstrated high quality HIV genotyping results from Asian laboratories.

Interlaboratory comparison of cytomegalovirus viral load assays

To assess interlaboratory variability in qualitative and quantitative cytomegalovirus (CMV) viral load (VL) testing, we distributed a panel of samples to 33 laboratories in the USA, Canada and Europe who performed testing using commercial reagents (n = 17) or laboratory-developed assays (n = 18). The panel included two negatives, seven samples constructed from purified CMV nucleocapsids in plasma (2.0-6.0 log(10) copies/mL) and three clinical plasma samples. Interlaboratory variation was observed in both actual (range, 2.0-4.0 log(10) copies/mL) and self-reported lower limits of detection (range, 1.0-4.0 log(10) copies/mL). Variation observed in reported results for individual samples ranged from 2.0 log(10) (minimum) to 4.3 log(10) (maximum)(.) Variation was greatest at low VLs. Assuming +/- 0.5 log(10) relative to the expected result represents an acceptable result, 57.6% of results fell within this range. Use of commercially available reagents and procedures was associated with less variability compared with laboratory-developed assays. Interlaboratory variability on replicate samples was significantly greater than intralaboratory variability (p < 0.0001). The significant interlaboratory variability in CMV VL observed may be impacting patient care and limiting interinstitutional comparisons. The creation of an international reference standard for CMV VL assay calibration would be an important step in quality improvement of this laboratory tool.

Evaluation of two avian influenza type A rapid antigen tests under Indonesian field conditions

The current study evaluated the test characteristics of 2 commercially available rapid antigen tests for highly pathogenic avian influenza. Diagnostic specimens were collected from free-ranging village chickens in Indonesia. A total of 174 healthy, sick, and dead birds were included in the study. The relative diagnostic test sensitivity and the relative diagnostic test specificity were calculated by using real-time reverse transcription polymerase chain reaction (RT-PCR) as the confirmatory diagnosis. The AnigenR Rapid AIV Ag test had a relative diagnostic sensitivity of 0.69 (95% confidence interval [CI]: 0.56-0.80) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). The Flu Detect(TM) Antigen Capture test strip had a relative diagnostic sensitivity of 0.71 (95% CI: 0.58-0.82) and a relative diagnostic specificity of 0.98 (95% CI: 0.93-0.99). These tests are a valuable tool for the Indonesian avian influenza control program by reliably and quickly detecting Influenza A virus from oropharyngeal swabs from sick or dying chickens.

Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays

BK virus (BKV) is the infectious cause of polyomavirus-associated nephropathy. Screening guidelines for renal-transplant recipients define levels of viremia and viruria that are actionable for additional testing or intervention. However, standardized real-time PCR primers, probes, and standards are unavailable, and the extent of agreement among published assays is unknown. We compared seven TaqMan real-time PCR primer/probe sets (three designed at this institution, three described in the literature, and one purchased) in conjunction with two different standards to prospectively measure BKV titers in 251 urine specimens submitted to our clinical laboratory. We observed substantial disagreement among assays attributable both to features of primer and probe design and to choice of reference material. The most significant source of error among individual specimens was primer or probe mismatch due to subtype-associated polymorphisms, primarily among subtype III and IV isolates. In contrast, measurement of the most abundant subtypes (Ia, V, and VI) were typically uniform among all seven assays. Finally, we describe and validate a new clinical assay designed to reliably measure all subtypes encountered in our study population (Ia, Ic, III, IV, and VI). Consideration of available BKV sequence information in conjunction with details of subtype distribution allowed us to develop a redesigned assay with markedly improved performance. These results suggest that both accurate BKV measurement and the uniform application of BKV screening guidelines could be significantly improved by the use of standardized reference materials and PCR primers and probes.

Performance evaluation of thermal cyclers for PCR in a rapid cycling condition

The performance of thermal cyclers for polymerase chain reactions (PCR) is of great concern in terms of the reliability of PCR-based assays, particularly when rapid cycling conditions are applied to small volume reactions. In this work, the precision of the temperature controls during rapid thermal cycling was measured in 19 commercial thermal cyclers of 8 different models. The temperatures of test solutions in specific locations in each thermal block were simultaneously monitored at 1 s intervals during thermal cycling. A temperature-sensitive multiplex PCR was run in parallel to assess undesirable PCR results caused by poor temperature control. Under the given conditions (20 s of annealing time and 20 µL reaction volume), a majority of the tested instruments showed prominent curving, undershooting, and/or overshooting in their temperature profiles, which substantially influenced the results of the temperature-sensitive multiplex PCR. Variations between wells were also observed in most instruments. It is strongly hoped that these problems will be addressed by manufacturers and that they will make substantial improvements in the precision and efficiency of thermal cyclers. In the meantime, users of thermal cyclers might be able to avoid unexpected poor outcomes of sensitive PCR-based assays by designing their PCR protocols with these findings in mind.

Comparison of performance characteristics of three real-time reverse transcription-PCR test systems for detection and quantification of hepatitis C virus

We evaluated the performance characteristics of three real-time reverse transcription-PCR test systems for detection and quantification of hepatitis C virus (HCV) and performed a direct comparison of the systems on the same clinical specimens. Commercial HCV panels (genotype 1b) were used to evaluate linear range, sensitivity, and precision. The Roche COBAS TaqMan HCV test for research use only (RUO) with samples processed on the MagNA Pure LC instrument (Roche RUO-MPLC) and Abbott analyte-specific reagents (ASR) with QIAGEN sample processing (Abbott ASR-Q) showed a sensitivity of 1.0 log(10) IU/ml with a linear dynamic range of 1.0 to 7.0 log(10) IU/ml. The Roche ASR in combination with the High Pure system (Roche ASR-HP) showed a sensitivity of 1.4 log(10) IU/ml with a linear dynamic range of 2.0 to 7.0 log(10) IU/ml. All of the systems showed acceptable reproducibility, the Abbott ASR-Q being the most reproducible of the three systems. Seventy-six clinical specimens (50 with detectable levels of HCV RNA and various titers and genotypes) were tested, and results were compared to those of the COBAS Amplicor HCV Monitor v2.0. Good correlation was obtained for the Roche RUO-MPLC and Abbott ASR-Q (R(2) = 0.84 and R(2) = 0.93, respectively), with better agreement for the Abbott ASR-Q. However, correlation (R(2) = 0.79) and agreement were poor for Roche ASR-HP, with bias relative to concentration and genotype. Roche ASR-HP underestimated HCV RNA for genotypes 3 and 4 as much as 2.19 log(10) IU/ml. Our study demonstrates that Roche RUO-MPLC and Abbott ASR-Q provided acceptable results and agreed sufficiently with the COBAS Amplicor HCV Monitor v2.0.

External quality assessment for the molecular detection of Hepatitis C virus

BACKGROUND, OBJECTIVES AND STUDY DESIGN: External quality assessment (EQA) panels were distributed internationally by UK NEQAS for Microbiology to 159 participants for the detection, quantification and genotyping of Hepatitis C virus (HCV) in freeze-dried plasma from 2000 to 2004. The results were analysed to determine the level of standardisation of qualitative detection, quantitative detection and genotyping.

RESULTS

The accurate detection of HCV in the panels varied from 86.9% to 100%. Four genotypes were distributed with the panels and there was no significant difference in the detection of different genotypes of HCV by participants. Further analysis indicated most variation occurred in quantification of HCV at lower concentrations and from 0% to 14.8% reported quantitative values outside 0.5 log(10) of the median value. In addition, three negative specimens were distributed and false positives were found to be rare (0.9-2.2%) with all methods included in the study.

CONCLUSION

The laboratory detection of HCV in plasma EQA specimens was varied, with decreasing parity of quantification at lower concentrations of HCV. False positives and negatives were rare, irrespective of the genotype under test.

Contamination with PCR detectable virus in a virus isolation quality assurance panel

External quality control schemes are an essential part of the quality assurance of all diagnostic virology laboratories. There are a few providers of nucleic acid detection quality control panels. Consequently, diagnostic laboratories may test panels that are developed specifically for virus isolation by nucleic acid detection methods. Here, we report on a recent simulated eye swab panel from a National external quality assessment service, which was meant for virus isolation but which we tested by polymerase chain reactions assays. The results suggest that the samples had been contaminated at source leading to difficulty in interpretation of the panel and a poor score.

Two quality control exercises involving nucleic acid amplification methods for detection of Mycoplasma pneumoniae and Chlamydophila pneumoniae and carried out 2 years apart (in 2002 and 2004)

The quality performance of laboratories for the detection of Mycoplasma pneumoniae and Chlamydophila pneumoniae by two quality control (QC) exercises with a 2-year interval was investigated. For the 2002 QC exercise, specimens were spiked with M. pneumoniae at concentrations of 5,000, 500, 50, and 0 color-changing units (CCU)/100 microl. The limit of detectability was 50 CCU/100 microl. Therefore, this concentration was omitted from the 2004 panel and was excluded from the analysis. In 2002, 2 out of 12 participants obtained 100% correct results, 2 out of 12 produced false-positive results, and 10 out of 12 had between 0 out of 9 and 8 out of 9 correct positive results. In 2004, correct results were obtained in 15 out of 18 tests, and no false-positive results were reported. In 2002, specimens were spiked with C. pneumoniae at concentrations of 490, 49, 4.9, and 0 inclusion-forming units/100 microl (IFU/100 microl). In the 2004 panel, samples spiked with a lower dilution of 0.49 IFU/100 microl were added to the panel. For the C. pneumoniae QC, correct results were produced in 12 out of 16 and 13 out of 18 tests in 2002 and in 2004, respectively. Both multiplex PCR and nucleic acid sequence-based amplification (NASBA) formats scored a smaller number of samples positive than the monoplex reactions.

Results of the first World Health Organization international collaborative study of detection of human papillomavirus DNA

Twenty-nine laboratories in 12 countries participated in a study to assess the performance of various human papillomavirus (HPV) detection assays through the use of a recombinant HPV DNA standard reagent panel. The panel was designed by a group of HPV experts, and samples were prepared and distributed by the World Health Organization International Laboratory for Standards and Biologicals in The Netherlands. Each panel consisted of 24 coded samples including a dilution series for HPV types 16 and 18, alone or in combination with five other high-risk (HR) HPV types including HPV types 31, 33, 35, 45, and 52, the low-risk HPV type 6, and a negative control. Qualitative assays were generally consistent across laboratories, and most invalid results reflected a lack of HPV test sensitivity. The combined data sets had a proficiency for HPV 16 of 62.5% (15/24) and for HPV 18 of 73.9% (17/23). HPV 31 was the least accurately detected by participating laboratories. Approximately half of participating laboratories failed to detect high concentrations of HPV 31 and, to a lesser extent, to detect HPV types 35, 52, and 6. The panel sample materials offer a source of renewable and reproducible material that could be used in the future development of international standard reagents for calibration of HPV DNA assays and kits.

Use of multiplex polymerase chain reactions to indicate the accuracy of the annealing temperature of thermal cycling

A condition for multiplex polymerase chain reactions (PCRs) of which outcomes sensitively indicate the actual annealing temperature of thermal cycling is reported. The multiplex reaction was designed to produce four different amplicons of 200, 300, 400, and 480 bp. However, the degree of amplification of each amplicon sensitively responds to a small change in the annealing temperature, by which one can predict the actual annealing temperature of thermal cycling. Deviations between the actual and the designated annealing temperatures as small as 0.5 degrees C were manifested by the banding patterns of the multiplex PCRs in simple agarose gel electrophoresis. For prediction of temperatures in a more objective manner, capillary electrophoresis was also applied to obtain numerical expressions of the relative intensities of the amplicons. By optimizing the multiplex PCR conditions, where concentrations of buffer, dNTPs, and primer pairs were major factors, satisfactory sensitivity and reproducibility of the band patterning were achieved. Blind tests demonstrated the accuracy of the prediction of actual annealing temperatures within +/-0.5 degrees C. The multiplex PCR approach will be further refined and tested for realization of an easily accessible alternative to a physical temperature measurement device in testing the performance of thermal cyclers for PCR.

A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses

Objectives

To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories.

Study design

Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected.

Results

All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory.

Conclusions

The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics.

External quality assessment for molecular detection of Bordetella pertussis in European laboratories

Although the PCR for the detection of Bordetella pertussis is routinely performed in diagnostic laboratories, no quality assessment program has so far been described. We report on the results obtained with two external quality assessment proficiency panels sent to European laboratories. The first proficiency panel contained a series of dilutions of three previously characterized B. pertussis clinical isolates and two negative controls. No false-positive results were reported by six laboratories providing seven data sets. The reported limits of detection of the three B. pertussis strains varied between 4 and 4,000, 9 and 9,000, and 3 and 30,000 CFU/ml, respectively. The second proficiency panel, composed of a series of dilutions of reference strains of B. pertussis, B. holmesii, B. hinzii, and B. bronchiseptica, as well as negative controls, was sent to nine laboratories. One laboratory reported a negative result for a sample and reported a B. parapertussis-positive sample to be positive for B. pertussis. By using the B. pertussis-specific target gene pertactin, one laboratory detected B. pertussis with 100% specificity. All other laboratories, which used IS481-based assays, reported positive results for the samples containing B. holmesii and B. bronchiseptica, species that have occasionally been recovered from human respiratory samples. These data show that the choice of the target gene is particularly critical for the species specificity of B. pertussis PCR assays.

Inter-laboratory comparison of qualitative and quantitative detection of hepatitis C (HCV) virus RNA in diagnostic virology: a multicentre study (MS) in Italy

BACKGROUND

The importance of the standardisation of nucleic acid amplification technology (NAT) assays for the detection of hepatitis C virus RNA is well known today, as many studies carried out in different European countries attest. The results of a previous study performed in Italy (J. Clin. Virol. 1 (2003) 83) by the Italian Society of Clinical Microbiology (AMCLI) showed that the use of external reference standards and of multicentre collaborative studies significantly improves laboratory performance for the qualitative evaluation of HCV RNA.

OBJECTIVES

the AMCLI organised a new study on the standardisation of both the qualitative and the quantitative evaluation of HCV RNA with NAT in order to improve the implementation of the diagnostic methods for HCV RNA detection.

STUDY DESIGN

seventeen diagnostic centres of major Italian Hospitals participated in this quality control study. The study consisted of testing three panels, each made up of 10 coded samples including negative and positive samples. Positive samples contained four levels of HCV RNA (genotype 1).

RESULTS AND CONCLUSION

Seven out of 510 qualitative results obtained were incorrect (1.4%), two false negative and five false positive. The results gave a sensitivity of 99.5% and a specificity of 95.8%. Regarding quantitative tests, the geometric mean (GM) and standard deviation (S.D.) could be calculated only for the three highest HCV RNA levels. The percentage of results within the range of GM +/- 0.5 log(10) varied from 91% to 100%. Some laboratories had some difficulty in the exact quantification of the lowest (3.00 log IU/ml) as well as of the highest viral levels (6.35 log IU/ml) values, very near to the limits of the dynamic range of the assays. The comparison of the results of this study with that previously carried out one confirms that a regular participation in external quality assessment (EQA) assures the achievement of a high proficiency level in the diagnosis of HCV infection.

Performance characteristics of a quantitative TaqMan hepatitis C virus RNA analyte-specific reagent

We determined the dynamic range, reproducibility, accuracy, genotype bias, and sensitivity of the TaqMan hepatitis C virus (HCV) analyte-specific reagent (ASR). Serum samples were processed using the MagNA Pure LC instrument and run on the COBAS TaqMan 48 analyzer. The performance characteristics of the ASR were also compared with those of the qualitative AMPLICOR and quantitative AMPLICOR MONITOR HCV tests. The ASR exhibited a >/=6-log(10) linear dynamic range and excellent reproducibility, with a mean coefficient of variation of 14%. HCV RNA concentration measured with the ASR agreed within an average of 0.42 log(10) (2.6-fold) of the labeled concentration with members of a standard reference panel. HCV genotypes 1 to 4 were amplified with similar efficiencies with the ASR. The ASR and AMPLICOR MONITOR viral load results were significantly correlated (r = 0.8898; P < 0.01), but the agreement was poor (mean difference, 0.45 +/- 0.35 log(10)) for 72 HCV RNA-positive clinical samples. However, 98.9% agreement between the ASR and qualitative AMPLICOR test results was found with 60 positive and 29 negative samples. Limiting-dilution experiments demonstrated that the limits of detection for ASR and AMPLICOR tests were 84 and 26 IU/ml, respectively. The performance characteristics of the TaqMan HCV ASR are appropriate for all clinical applications of HCV RNA testing.

Multicentre quality control study for detection of Mycobacterium tuberculosis in clinical samples by nucleic amplification methods

The aim of this study was to evaluate the laboratory performance of nucleic acid amplification tests (NATs) for detection of the Mycobacterium tuberculosis complex. A proficiency panel consisting of eight sputum specimens and four specimens diluted in phosphate-buffered saline (PBS) was sent to 82 laboratories in 23 countries by the Quality Control for Molecular Diagnostics (QCMD) TB programme. The performance of different NATs was analysed in combination with a questionnaire on the applied methods. Seventy-eight participants (95.2%) contributed a total of 85 evaluable data sets. The percentage of correct results on the eight sputum samples was 86.3% (586/679). Of the sputum specimens considered as 'smear-negatives' (650 CFU/250 micro L), only 61.2% (104/170) were reported positive. The percentage of correct results for the three scored PBS samples was 75.7% (193/255). The total number of false-positive results was 11 (4.3%); these were reported for seven (8.2%) of the 85 data sets. In 32 (37.6%) data sets an 'in-house' NAT method was used, and in 53 (62.4%) sets a commercial assay was tested. The percentage of data sets achieving correct results on all sputum samples was 35.3% and 37.8%, respectively. For the PBS samples this was 45.8% and 41.5%. Overall, the results of this study demonstrated that the performance of NATs for the detection of M. tuberculosis has improved since previous studies. The percentage of false-positives has decreased considerably. However, a large number of procedures still lack sufficient sensitivity for application to smear-negative samples.

Introducing a molecular test into the clinical microbiology laboratory: development, evaluation, and validation

CONTEXT

In the mid-1980s, the polymerase chain reaction methodology for the amplification of minute amounts of target DNA was successfully developed and then introduced into clinical use; such technology has led to a revolution in diagnostic testing. Despite enormous advances in the detection of infectious agents by amplification methods, there are also limitations that must be addressed.

OBJECTIVE

To highlight the pertinent steps and issues associated with the introduction of an amplification assay into a clinical microbiology laboratory as well as the subsequent ongoing activities following its introduction into routine laboratory use.

DATA SOURCES

Data were obtained from literature searches from 1990 through September 2002 using the subject headings "polymerase chain reaction," "molecular assays," and "amplification" as well as publications of the National Committee for Clinical Laboratory Standards.

DATA EXTRACTION AND SYNTHESIS

Using the findings obtained from these studies and publications, the process of introducing a molecular assay into the clinical microbiology laboratory was broken down into 4 major components: (1) initial phase of assay development, (2) polymerase chain reaction assay verification in which analytic sensitivity and specificity is determined, (3) assay validation to determine clinical sensitivity and specificity, and (4) interpretation of results and ongoing, required activities. The approach, as well as the advantages and limitations involved in each step of the process, was highlighted and discussed within the context of the published literature.

CONCLUSIONS

The application of molecular testing methods in the clinical laboratory has dramatically improved our ability to diagnose infectious diseases. However, the clinical usefulness of molecular testing will only be maximized to its fullest benefit by appropriate and careful studies correlating clinical findings with assay results.

Quality control in nucleic acid testing--where do we stand?

Quality control has been playing an increasingly important role in the implementation of nucleic acid amplification techniques (NATs) for clinical diagnosis since the introduction of these methods in the early 1990s. Initial multicenter studies involving hepatitis B virus (HBV), hepatitis C virus (HCV), Mycobacterium tuberculosis, and human immunodeficiency virus type 1 (HIV-1) revealed serious problems in specificity (false-positive rates of ca. 40%) and sensitivity, large variations in quantitative results, and a plethora of units (largely not comparable between assays). The problem areas identified included the need for standardized reagents and common units, contamination control mechanisms, inhibition control mechanisms, genotype-independent detection and quantitation, facilitated nucleic acid isolation procedures, clinically relevant dynamic ranges, and internal run controls. Progress made in each of these areas will be discussed. In addition to the above-mentioned problem areas, the value of external quality control of existing and evolving NATs was recognized. To this end, the European Union Quality Control Concerted Action for Nucleic Acid Amplification in Diagnostic Virology was established in May 1998. During its three-and-a-half years of existence, a total of 14 proficiency panels containing 8-13 well-characterized, simulated clinical samples of various viral loads and genotypes were prepared for herpesviruses (herpes simplex virus, human cytomegalovirus), blood-borne viruses (HBV, HCV, HIV-1), enteroviruses, and Chlamydia trachomatis, distributed to up to 20 different countries, and tested by up to 97 different laboratories. The results show dramatic improvement in specificity (false-positive rates <3% for most panels), presumably due to a generally greater expertise of participating laboratories, more frequent use of enzymatic or mechanical contamination control mechanisms, and increased utilization of standardized reagents (commercial kits). However, considerable problems with sensitivity remain (false-negative rates up to 50%), reflecting the high detection limits of some commercial viral load kits still on the market as well as inadequate standardization of quantitation controls between assay systems. In conclusion, although considerable progress has been made, quality control of NATs in clinical diagnosis remains an ongoing challenge.